From c76d69d30da741538c2428b4b255103528880fb2 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Feb 2024 15:29:59 +0000 Subject: [PATCH 01/40] Template update for nf-core/tools version 2.13 --- .editorconfig | 9 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/ci.yml | 7 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 17 +- .github/workflows/linting.yml | 12 +- .github/workflows/linting_comment.yml | 4 +- .github/workflows/release-announcements.yml | 11 +- README.md | 5 +- assets/multiqc_config.yml | 2 + assets/schema_input.json | 21 +- bin/check_samplesheet.py | 259 ----------- conf/modules.config | 8 - lib/NfcoreTemplate.groovy | 356 -------------- lib/Utils.groovy | 47 -- lib/WorkflowMain.groovy | 77 --- lib/WorkflowReadsimulator.groovy | 122 ----- main.nf | 100 ++-- modules.json | 28 +- modules/local/samplesheet_check.nf | 31 -- .../dumpsoftwareversions/environment.yml | 7 - .../custom/dumpsoftwareversions/main.nf | 24 - .../custom/dumpsoftwareversions/meta.yml | 37 -- .../templates/dumpsoftwareversions.py | 102 ---- .../dumpsoftwareversions/tests/main.nf.test | 43 -- .../tests/main.nf.test.snap | 33 -- .../dumpsoftwareversions/tests/tags.yml | 2 - modules/nf-core/fastqc/tests/main.nf.test | 14 +- .../nf-core/fastqc/tests/main.nf.test.snap | 76 ++- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/tests/main.nf.test | 13 +- .../nf-core/multiqc/tests/main.nf.test.snap | 32 +- nextflow.config | 5 +- nextflow_schema.json | 1 + pyproject.toml | 8 +- subworkflows/local/input_check.nf | 44 -- .../main.nf | 247 ++++++++++ .../nf-core/utils_nextflow_pipeline/main.nf | 126 +++++ .../nf-core/utils_nextflow_pipeline/meta.yml | 38 ++ .../tests/main.function.nf.test | 54 +++ .../tests/main.function.nf.test.snap | 12 + .../tests/main.workflow.nf.test | 123 +++++ .../tests/nextflow.config | 9 + .../utils_nextflow_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfcore_pipeline/main.nf | 440 ++++++++++++++++++ .../nf-core/utils_nfcore_pipeline/meta.yml | 24 + .../tests/main.function.nf.test | 134 ++++++ .../tests/main.function.nf.test.snap | 138 ++++++ .../tests/main.workflow.nf.test | 29 ++ .../tests/main.workflow.nf.test.snap | 15 + .../tests/nextflow.config | 9 + .../utils_nfcore_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfvalidation_plugin/main.nf | 62 +++ .../utils_nfvalidation_plugin/meta.yml | 44 ++ .../tests/main.nf.test | 200 ++++++++ .../tests/nextflow_schema.json | 96 ++++ .../utils_nfvalidation_plugin/tests/tags.yml | 2 + workflows/readsimulator.nf | 133 ++---- 61 files changed, 2108 insertions(+), 1406 deletions(-) delete mode 100755 bin/check_samplesheet.py delete mode 100755 lib/NfcoreTemplate.groovy delete mode 100644 lib/Utils.groovy delete mode 100755 lib/WorkflowMain.groovy delete mode 100755 lib/WorkflowReadsimulator.groovy delete mode 100644 modules/local/samplesheet_check.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml delete mode 100644 subworkflows/local/input_check.nf create mode 100644 subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 9b99008..dd9ffa5 100644 --- a/.editorconfig +++ b/.editorconfig @@ -18,7 +18,12 @@ end_of_line = unset insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset -indent_size = unset +[/subworkflows/nf-core/**] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset [/assets/email*] indent_size = unset @@ -28,5 +33,5 @@ indent_size = unset indent_style = unset # ignore python -[*.{py}] +[*.{py,md}] indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index bd01c3d..8afecca 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index ed0d641..eea16df 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index c2775b1..2bdf802 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v2 + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3590023..871de61 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,13 +28,16 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 with: version: "${{ matrix.NXF_VER }}" + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index e37cfda..0b6b1f2 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v9 + - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 8611458..f823210 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download' # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core download." + required: true + default: "dev" pull_request: types: - opened @@ -23,13 +28,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" - - uses: eWaterCycle/setup-singularity@v7 + - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: singularity-version: 3.8.3 @@ -42,13 +47,13 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./ run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ @@ -64,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 81cd098..748b431 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Set up Python 3.11 - uses: actions/setup-python@v5 + uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: 3.11 cache: "pip" @@ -32,12 +32,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 147bcd1..b706875 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v3 + uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 + uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 21ac3f0..c3674af 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -9,6 +9,11 @@ jobs: toot: runs-on: ubuntu-latest steps: + - name: get topics and convert to hashtags + id: get_topics + run: | + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -20,11 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} + ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +63,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.1.0 + - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/README.md b/README.md index 78caf82..7088cc8 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,9 @@ nf-core/readsimulator -[![GitHub Actions CI Status](https://github.com/nf-core/readsimulator/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/readsimulator/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/readsimulator/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/readsimulator/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/readsimulator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) + +[![GitHub Actions CI Status](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/readsimulator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 9491aa7..c3ad8a7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -13,3 +13,5 @@ report_section_order: order: -1002 export_plots: true + +disable_version_detection: true diff --git a/assets/schema_input.json b/assets/schema_input.json index 51606d1..33e4478 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,25 +10,22 @@ "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] }, "fastq_1": { "type": "string", + "format": "file-path", + "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ] + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, "required": ["sample", "fastq_1"] diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index 4a758fe..0000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,259 +0,0 @@ -#!/usr/bin/env python - - -"""Provide a command line tool to validate and transform tabular samplesheets.""" - - -import argparse -import csv -import logging -import sys -from collections import Counter -from pathlib import Path - -logger = logging.getLogger() - - -class RowChecker: - """ - Define a service that can validate and transform each given row. - - Attributes: - modified (list): A list of dicts, where each dict corresponds to a previously - validated and transformed row. The order of rows is maintained. - - """ - - VALID_FORMATS = ( - ".fq.gz", - ".fastq.gz", - ) - - def __init__( - self, - sample_col="sample", - first_col="fastq_1", - second_col="fastq_2", - single_col="single_end", - **kwargs, - ): - """ - Initialize the row checker with the expected column names. - - Args: - sample_col (str): The name of the column that contains the sample name - (default "sample"). - first_col (str): The name of the column that contains the first (or only) - FASTQ file path (default "fastq_1"). - second_col (str): The name of the column that contains the second (if any) - FASTQ file path (default "fastq_2"). - single_col (str): The name of the new column that will be inserted and - records whether the sample contains single- or paired-end sequencing - reads (default "single_end"). - - """ - super().__init__(**kwargs) - self._sample_col = sample_col - self._first_col = first_col - self._second_col = second_col - self._single_col = single_col - self._seen = set() - self.modified = [] - - def validate_and_transform(self, row): - """ - Perform all validations on the given row and insert the read pairing status. - - Args: - row (dict): A mapping from column headers (keys) to elements of that row - (values). - - """ - self._validate_sample(row) - self._validate_first(row) - self._validate_second(row) - self._validate_pair(row) - self._seen.add((row[self._sample_col], row[self._first_col])) - self.modified.append(row) - - def _validate_sample(self, row): - """Assert that the sample name exists and convert spaces to underscores.""" - if len(row[self._sample_col]) <= 0: - raise AssertionError("Sample input is required.") - # Sanitize samples slightly. - row[self._sample_col] = row[self._sample_col].replace(" ", "_") - - def _validate_first(self, row): - """Assert that the first FASTQ entry is non-empty and has the right format.""" - if len(row[self._first_col]) <= 0: - raise AssertionError("At least the first FASTQ file is required.") - self._validate_fastq_format(row[self._first_col]) - - def _validate_second(self, row): - """Assert that the second FASTQ entry has the right format if it exists.""" - if len(row[self._second_col]) > 0: - self._validate_fastq_format(row[self._second_col]) - - def _validate_pair(self, row): - """Assert that read pairs have the same file extension. Report pair status.""" - if row[self._first_col] and row[self._second_col]: - row[self._single_col] = False - first_col_suffix = Path(row[self._first_col]).suffixes[-2:] - second_col_suffix = Path(row[self._second_col]).suffixes[-2:] - if first_col_suffix != second_col_suffix: - raise AssertionError("FASTQ pairs must have the same file extensions.") - else: - row[self._single_col] = True - - def _validate_fastq_format(self, filename): - """Assert that a given filename has one of the expected FASTQ extensions.""" - if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): - raise AssertionError( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) - - def validate_unique_samples(self): - """ - Assert that the combination of sample name and FASTQ filename is unique. - - In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the - number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. - - """ - if len(self._seen) != len(self.modified): - raise AssertionError("The pair of sample name and FASTQ must be unique.") - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - row[self._sample_col] = f"{sample}_T{seen[sample]}" - - -def read_head(handle, num_lines=10): - """Read the specified number of lines from the current position in the file.""" - lines = [] - for idx, line in enumerate(handle): - if idx == num_lines: - break - lines.append(line) - return "".join(lines) - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - Check that the tabular samplesheet has the structure expected by nf-core pipelines. - - Validate the general shape of the table, expected columns, and each row. Also add - an additional column which records whether one or two FASTQ reads were found. - - Args: - file_in (pathlib.Path): The given tabular samplesheet. The format can be either - CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. - file_out (pathlib.Path): Where the validated and transformed samplesheet should - be created; always in CSV format. - - Example: - This function checks that the samplesheet follows the following structure, - see also the `viral recon samplesheet`_:: - - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - - .. _viral recon samplesheet: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - - """ - required_columns = {"sample", "fastq_1", "fastq_2"} - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_in.open(newline="") as in_handle: - reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) - # Validate the existence of the expected header columns. - if not required_columns.issubset(reader.fieldnames): - req_cols = ", ".join(required_columns) - logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") - sys.exit(1) - # Validate each row. - checker = RowChecker() - for i, row in enumerate(reader): - try: - checker.validate_and_transform(row) - except AssertionError as error: - logger.critical(f"{str(error)} On line {i + 2}.") - sys.exit(1) - checker.validate_unique_samples() - header = list(reader.fieldnames) - header.insert(1, "single_end") - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_out.open(mode="w", newline="") as out_handle: - writer = csv.DictWriter(out_handle, header, delimiter=",") - writer.writeheader() - for row in checker.modified: - writer.writerow(row) - - -def parse_args(argv=None): - """Define and immediately parse command line arguments.""" - parser = argparse.ArgumentParser( - description="Validate and transform a tabular samplesheet.", - epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", - ) - parser.add_argument( - "file_in", - metavar="FILE_IN", - type=Path, - help="Tabular input samplesheet in CSV or TSV format.", - ) - parser.add_argument( - "file_out", - metavar="FILE_OUT", - type=Path, - help="Transformed output samplesheet in CSV format.", - ) - parser.add_argument( - "-l", - "--log-level", - help="The desired log level (default WARNING).", - choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), - default="WARNING", - ) - return parser.parse_args(argv) - - -def main(argv=None): - """Coordinate argument parsing and program execution.""" - args = parse_args(argv) - logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") - if not args.file_in.is_file(): - logger.error(f"The given input file {args.file_in} was not found!") - sys.exit(2) - args.file_out.parent.mkdir(parents=True, exist_ok=True) - check_samplesheet(args.file_in, args.file_out) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/conf/modules.config b/conf/modules.config index d91c6ab..e3ea8fa 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,14 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: FASTQC { ext.args = '--quiet' } diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index e248e4c..0000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,356 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" - } - } - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); - output_tf.delete() - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4..0000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index 477ddaf..0000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,77 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/readsimulator pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log, args) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - // Check that the profile doesn't contain spaces and doesn't end with a trailing comma - checkProfile(workflow.profile, args, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - } - } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } - - // - // Exit pipeline if --profile contains spaces - // - private static void checkProfile(profile, args, log) { - if (profile.endsWith(',')) { - Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - if (args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - } -} diff --git a/lib/WorkflowReadsimulator.groovy b/lib/WorkflowReadsimulator.groovy deleted file mode 100755 index 9dd5e20..0000000 --- a/lib/WorkflowReadsimulator.groovy +++ /dev/null @@ -1,122 +0,0 @@ -// -// This file holds several functions specific to the workflow/readsimulator.nf in the nf-core/readsimulator pipeline -// - -import nextflow.Nextflow -import groovy.text.SimpleTemplateEngine - -class WorkflowReadsimulator { - - // - // Check and validate parameters - // - public static void initialise(params, log) { - - genomeExistsError(params, log) - - - if (!params.fasta) { - Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - } - } - - // - // Get workflow summary for MultiQC - // - public static String paramsSummaryMultiqc(workflow, summary) { - String summary_section = '' - for (group in summary.keySet()) { - def group_params = summary.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

$group

\n" - summary_section += "
\n" - for (param in group_params.keySet()) { - summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" - } - summary_section += "
\n" - } - } - - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - return yaml_file_text - } - - // - // Generate methods description for MultiQC - // - - public static String toolCitationText(params) { - - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text - } - - public static String toolBibliographyText(params) { - - // TODO Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
  • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
  • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
  • " - ].join(' ').trim() - - return reference_text - } - - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = run_workflow.toMap() - meta["manifest_map"] = run_workflow.manifest.toMap() - - // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
  • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - //meta["tool_bibliography"] = toolBibliographyText(params) - - - def methods_text = mqc_methods_yaml.text - - def engine = new SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html - } - - // - // Exit pipeline if incorrect --genome key provided - // - private static void genomeExistsError(params, log) { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - } - } -} diff --git a/main.nf b/main.nf index 020f9fc..863375d 100644 --- a/main.nf +++ b/main.nf @@ -13,66 +13,96 @@ nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') +include { READSIMULATOR } from './workflows/readsimulator' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_readsimulator_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_readsimulator_pipeline' + +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_readsimulator_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE & PRINT PARAMETER SUMMARY + GENOME PARAMETER VALUES ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { validateParameters; paramsHelp } from 'plugin/nf-validation' - -// Print help message if needed -if (params.help) { - def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) - def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - -WorkflowMain.initialise(workflow, params, log, args) +// TODO nf-core: Remove this line if you don't need a FASTA file +// This is an example of how to use getGenomeAttribute() to fetch parameters +// from igenomes.config using `--genome` +params.fasta = getGenomeAttribute('fasta') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOW FOR PIPELINE + NAMED WORKFLOWS FOR PIPELINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { READSIMULATOR } from './workflows/readsimulator' - // -// WORKFLOW: Run main nf-core/readsimulator analysis pipeline +// WORKFLOW: Run main analysis pipeline depending on type of input // workflow NFCORE_READSIMULATOR { - READSIMULATOR () -} + take: + samplesheet // channel: samplesheet read in from --input + + main: + + // + // WORKFLOW: Run pipeline + // + READSIMULATOR ( + samplesheet + ) + + emit: + multiqc_report = READSIMULATOR.out.multiqc_report // channel: /path/to/multiqc_report.html + +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN ALL WORKFLOWS + RUN MAIN WORKFLOW ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// WORKFLOW: Execute a single named workflow for the pipeline -// See: https://github.com/nf-core/rnaseq/issues/619 -// workflow { - NFCORE_READSIMULATOR () + + main: + + // + // SUBWORKFLOW: Run initialisation tasks + // + PIPELINE_INITIALISATION ( + params.version, + params.help, + params.validate_params, + params.monochrome_logs, + args, + params.outdir, + params.input + ) + + // + // WORKFLOW: Run main workflow + // + NFCORE_READSIMULATOR ( + PIPELINE_INITIALISATION.out.samplesheet + ) + + // + // SUBWORKFLOW: Run completion tasks + // + PIPELINE_COMPLETION ( + params.email, + params.email_on_fail, + params.plaintext_email, + params.outdir, + params.monochrome_logs, + params.hook_url, + NFCORE_READSIMULATOR.out.multiqc_report + ) } /* diff --git a/modules.json b/modules.json index 39ebfe9..f9a957e 100644 --- a/modules.json +++ b/modules.json @@ -5,22 +5,36 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] - }, "fastqc": { "branch": "master", - "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", + "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", + "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "installed_by": ["subworkflows"] + }, + "utils_nfvalidation_plugin": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 12b03cf..0000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/readsimulator/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml deleted file mode 100644 index 9b3272b..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: custom_dumpsoftwareversions -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index f218761..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index 5f15a5f..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,37 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" -maintainers: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100755 index e55b8d4..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - - -import platform -from textwrap import dedent - -import yaml - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - - - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index b1e1630..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,43 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.mqc_yml[0]).readLines()[0..10], - file(process.out.yml[0]).readLines()[0..7] - ).match() - } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 5f59a93..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "Should run without failures": { - "content": [ - [ - "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" - ], - [ - "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", - " \\n\\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n \\n \\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n\\n\\n \\n\\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 1f21c66..70edae4 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -63,7 +63,7 @@ nextflow_process { { assert path(process.out.html[0][1][0]).text.contains("") }, { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -89,7 +89,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -115,7 +115,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -153,7 +153,7 @@ nextflow_process { { assert path(process.out.html[0][1][2]).text.contains("") }, { assert path(process.out.html[0][1][3]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -179,7 +179,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } @@ -204,7 +204,7 @@ nextflow_process { { assert process.success }, { assert snapshot(process.out.html.collect { file(it[1]).getName() } + process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match() } + process.out.versions ).match("fastqc_stub") } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 5d624bb..86f7c31 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,5 +1,17 @@ { - "sarscov2 single-end [fastq] - stub": { + "fastqc_versions_interleaved": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:07.293713" + }, + "fastqc_stub": { "content": [ [ "test.html", @@ -7,14 +19,70 @@ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:40:57.254299" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:31:01.425198" + }, + "fastqc_versions_multiple": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:55.797907" + }, + "fastqc_versions_bam": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:26.795862" + }, + "fastqc_versions_single": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:27.043675" + }, + "fastqc_versions_paired": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:47.584191" }, - "versions": { + "fastqc_versions_custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:36:50.033627" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 7625b75..2212096 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1b9f7c4..354f443 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index d0438ed..f1c4242 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + tag "modules" tag "modules_nfcore" tag "multiqc" @@ -12,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -25,7 +26,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_single") } ) } @@ -36,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] @@ -49,7 +50,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_config") } ) } } @@ -61,7 +62,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -75,7 +76,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match() } + process.out.versions ).match("multiqc_stub") } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index d37e730..c204b48 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,21 +1,41 @@ { - "versions": { + "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:02:49.911994" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:28:51.744211298" }, - "sarscov2 single-end [fastqc] - stub": { + "multiqc_stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:03:14.524346" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:28.847433492" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:13.223621555" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 47b6d8f..f4bd23f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,9 +16,7 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - - - // MultiQC options + fasta = null// MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null @@ -43,7 +41,6 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options // Defaults only, expecting to be overwritten diff --git a/nextflow_schema.json b/nextflow_schema.json index 4059444..d5dce48 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,6 +16,7 @@ "type": "string", "format": "file-path", "exists": true, + "schema": "assets/schema_input.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", diff --git a/pyproject.toml b/pyproject.toml index 7d08e1c..5611062 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,11 +3,13 @@ [tool.ruff] line-length = 120 target-version = "py38" -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] cache-dir = "~/.cache/ruff" -[tool.ruff.isort] +[tool.ruff.lint] +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] + +[tool.ruff.lint.isort] known-first-party = ["nf_core"] -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 0aecf87..0000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,44 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - - main: - SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it) } - .set { reads } - - emit: - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row) { - // create meta map - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} diff --git a/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf new file mode 100644 index 0000000..dc90ad9 --- /dev/null +++ b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf @@ -0,0 +1,247 @@ +// +// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { fromSamplesheet } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + help // boolean: Display help text + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + input // string: Path to input samplesheet + + main: + + ch_versions = Channel.empty() + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFVALIDATION_PLUGIN ( + help, + workflow_command, + pre_help_text, + post_help_text, + validate_params, + "nextflow_schema.json" + ) + + // + // Check config provided to the pipeline + // + UTILS_NFCORE_PIPELINE ( + nextflow_cli_args + ) + // + // Custom validation for pipeline parameters + // + validateInputParameters() + + // + // Create channel from input file provided through params.input + // + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + validateInputSamplesheet(it) + } + .map { + meta, fastqs -> + return [ meta, fastqs.flatten() ] + } + .set { ch_samplesheet } + + emit: + samplesheet = ch_samplesheet + versions = ch_versions +} + +/* +======================================================================================== + SUBWORKFLOW FOR PIPELINE COMPLETION +======================================================================================== +*/ + +workflow PIPELINE_COMPLETION { + + take: + email // string: email address + email_on_fail // string: email address sent on pipeline failure + plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output + hook_url // string: hook URL for notifications + multiqc_report // string: Path to MultiQC report + + main: + + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + } + + completionSummary(monochrome_logs) + + if (hook_url) { + imNotification(summary_params, hook_url) + } + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ +// +// Check and validate pipeline parameters +// +def validateInputParameters() { + genomeExistsError() +}// +// Validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] +} +// +// Get attribute from genome config file e.g. fasta +// +def getGenomeAttribute(attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null +} + +// +// Exit pipeline if incorrect --genome key provided +// +def genomeExistsError() { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +}// +// Generate methods description for MultiQC +// +def toolCitationText() { + // TODO nf-core: Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text +} + +def toolBibliographyText() { + // TODO nf-core: Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
  • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
  • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
  • " + ].join(' ').trim() + + return reference_text +} + +def methodsDescriptionText(mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = workflow.toMap() + meta["manifest_map"] = workflow.manifest.toMap() + + // Pipeline DOI + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
  • " + + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + // meta["tool_bibliography"] = toolBibliographyText() + + + def methods_text = mqc_methods_yaml.text + + def engine = new groovy.text.SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html.toString() +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 0000000..ac31f28 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,126 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 0000000..e5c3a0a --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 0000000..8ed4310 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 0000000..db2030f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,12 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "timestamp": "2024-01-19T11:32:36.031083" + }, + "Test Function checkCondaChannels": { + "content": null, + "timestamp": "2024-01-19T11:32:50.456" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 0000000..f7c54bc --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,123 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } + ) + } + } + + test("Should dump params") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = params.outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = null + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 0000000..53574ff --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 0000000..f847611 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 0000000..a8b55d6 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,440 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +import org.yaml.snakeyaml.Yaml +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFCORE_PIPELINE { + + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + valid_config = true + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } + if (nextflow_cli_args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } +} + +// +// Citation string for pipeline +// +def workflowCitation() { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + " ${workflow.manifest.doi}\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + Yaml yaml = new Yaml() + versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + $workflow.manifest.name: ${getWorkflowVersion()} + Nextflow: $workflow.nextflow.version + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions + .unique() + .map { processVersionsFromYAML(it) } + .unique() + .mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + for (group in summary_params.keySet()) { + def group_params = summary_params.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    $group

    \n" + summary_section += "
    \n" + for (param in group_params.keySet()) { + summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Attach the multiqc report to email +// +def attachMultiqcReport(multiqc_report) { + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + return mqc_report +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = attachMultiqcReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = logColours(monochrome_logs) + if (email_address) { + try { + if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 0000000..d08d243 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 0000000..1dc317f --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,134 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 0000000..10f948e --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,138 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "timestamp": "2024-02-09T15:43:55.145717" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "timestamp": "2024-01-19T11:34:13.548431224" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "timestamp": "2024-01-19T11:34:38.840454873" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "timestamp": "2024-01-19T11:34:22.24352016" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "timestamp": "2024-01-19T11:35:04.418416984" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "timestamp": "2024-01-19T11:34:55.420000755" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "timestamp": "2024-01-19T11:35:13.436366565" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 0000000..8940d32 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 0000000..d07ce54 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,15 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "timestamp": "2024-01-19T11:35:22.538940073" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 0000000..d0a926b --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 0000000..ac8523c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf new file mode 100644 index 0000000..2585b65 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-validation' +include { validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFVALIDATION_PLUGIN { + + take: + print_help // boolean: print help + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // boolean: validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml new file mode 100644 index 0000000..3d4a6b0 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFVALIDATION_PLUGIN" +description: Use nf-validation to initiate and validate a pipeline +keywords: + - utility + - pipeline + - initialise + - validation +components: [] +input: + - print_help: + type: boolean + description: | + Print help message and exit + - workflow_command: + type: string + description: | + The command to run the workflow e.g. "nextflow run main.nf" + - pre_help_text: + type: string + description: | + Text to print before the help message + - post_help_text: + type: string + description: | + Text to print after the help message + - validate_params: + type: boolean + description: | + Validate the parameters and error if invalid. + - schema_filename: + type: string + description: | + The filename of the schema to validate against. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test new file mode 100644 index 0000000..517ee54 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -0,0 +1,200 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + script "../main.nf" + workflow "UTILS_NFVALIDATION_PLUGIN" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "plugin/nf-validation" + tag "'plugin/nf-validation'" + tag "utils_nfvalidation_plugin" + tag "subworkflows/utils_nfvalidation_plugin" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with command") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('pre-help-text') } }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } }, + { assert workflow.stdout.any { it.contains('post-help-text') } } + ) + } + } + + test("Should validate params") { + + when { + + params { + monochrome_logs = true + test_data = '' + outdir = 1 + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json new file mode 100644 index 0000000..7626c1c --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml new file mode 100644 index 0000000..60b1cff --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfvalidation_plugin: + - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/readsimulator.nf b/workflows/readsimulator.nf index fc09a0a..276dec0 100644 --- a/workflows/readsimulator.nf +++ b/workflows/readsimulator.nf @@ -1,54 +1,15 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowReadsimulator.initialise(params, log) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT LOCAL MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules -// -include { INPUT_CHECK } from '../subworkflows/local/input_check' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT NF-CORE MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Installed directly from nf-core/modules -// -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_readsimulator_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -56,50 +17,45 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Info required for completion email and summary -def multiqc_report = [] - workflow READSIMULATOR { - ch_versions = Channel.empty() + take: + ch_samplesheet // channel: samplesheet read in from --input - // - // SUBWORKFLOW: Read in samplesheet, validate and stage input files - // - INPUT_CHECK ( - file(params.input) - ) - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema + main: + + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() // // MODULE: Run FastQC // FASTQC ( - INPUT_CHECK.out.reads + ch_samplesheet ) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + .set { ch_collated_versions } // // MODULE: MultiQC // - workflow_summary = WorkflowReadsimulator.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowReadsimulator.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) MULTIQC ( ch_multiqc_files.collect(), @@ -107,31 +63,10 @@ workflow READSIMULATOR { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - multiqc_report = MULTIQC.out.report.toList() -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} -workflow.onError { - if (workflow.errorReport.contains("Process requirement exceeds available memory")) { - println("🛑 Default resources exceed availability 🛑 ") - println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") - } + emit: + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From e7168fdd36d5721260b761d0271e5d074b80cf7e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 29 Feb 2024 16:11:38 +0000 Subject: [PATCH 02/40] Template update for nf-core/tools version 2.13.1 --- .devcontainer/devcontainer.json | 10 +---- .github/CONTRIBUTING.md | 14 ++++--- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/ci.yml | 2 +- .github/workflows/download_pipeline.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .gitpod.yml | 6 +-- README.md | 3 +- modules.json | 8 ++-- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 12 +++--- .../main.nf | 10 +++-- .../tests/main.function.nf.test | 2 +- .../tests/main.function.nf.test.snap | 12 +++++- .../tests/main.workflow.nf.test | 20 ++------- .../tests/nextflow.config | 2 +- .../tests/main.function.nf.test.snap | 42 +++++++++++++++---- .../tests/main.workflow.nf.test.snap | 6 ++- .../tests/main.nf.test | 2 +- 23 files changed, 99 insertions(+), 74 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe..b290e09 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,15 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.defaultInterpreterPath": "/opt/conda/bin/python" }, // Add the IDs of extensions you want installed when the container is created. diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 25e2fd5..8c9d450 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,9 +9,8 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -:::info -If you need help using or modifying nf-core/readsimulator then the best place to ask is on the nf-core Slack [#readsimulator](https://nfcore.slack.com/channels/readsimulator) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: +> [!NOTE] +> If you need help using or modifying nf-core/readsimulator then the best place to ask is on the nf-core Slack [#readsimulator](https://nfcore.slack.com/channels/readsimulator) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow @@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. @@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`. Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. +The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. ### Naming schemes diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 440b520..228534d 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/read - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/readsimulator/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/readsimulator _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8afecca..bd01c3d 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index eea16df..ed0d641 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 871de61..888247a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index f823210..08622fd 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 748b431..073e187 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c3674af..d468aea 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.gitpod.yml b/.gitpod.yml index 363d5b1..105a182 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -10,13 +10,11 @@ tasks: vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code + - charliermarsh.ruff # Code linter Ruff diff --git a/README.md b/README.md index 7088cc8..3bcacc0 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,13 @@ [![GitHub Actions CI Status](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/readsimulator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/readsimulator) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/readsimulator) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23readsimulator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/readsimulator)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/modules.json b/modules.json index f9a957e..d375029 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2212096..ca39fb6 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 354f443..47ac352 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index c204b48..bfebd80 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:28:51.744211298" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:28.847433492" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:13.223621555" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf index dc90ad9..da28197 100644 --- a/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// Subworkflow with functionality specific to the nf-core/readsimulator pipeline // /* @@ -152,7 +152,9 @@ workflow PIPELINE_COMPLETION { // def validateInputParameters() { genomeExistsError() -}// +} + +// // Validate channels from input samplesheet // def validateInputSamplesheet(input) { @@ -190,7 +192,9 @@ def genomeExistsError() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } -}// +} + +// // Generate methods description for MultiQC // def toolCitationText() { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310..68718e4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f..e3f0baf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index f7c54bc..ca964ce 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -68,19 +62,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +87,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ff..d0a926b 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -6,4 +6,4 @@ manifest { nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 10f948e..1037232 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -1,25 +1,41 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" }, "Test Function nfCoreLogo": { "content": [ "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" ], - "timestamp": "2024-01-19T11:34:38.840454873" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" }, "Test Function workflowCitation": { "content": [ "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" }, "Test Function without logColours": { "content": [ @@ -73,13 +89,21 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function dashedLine": { "content": [ "-\u001b[2m----------------------------------------------------\u001b[0m-" ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" }, "Test Function with logColours": { "content": [ @@ -133,6 +157,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54..859d103 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 517ee54..5784a33 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -197,4 +197,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +} From 25f91c9269a1ff5f0a8038cb9c0c5d58b4b92d4d Mon Sep 17 00:00:00 2001 From: Carson J Miller Date: Wed, 13 Mar 2024 23:55:31 +0000 Subject: [PATCH 03/40] Added option to take draft genomes for insilicoseq --- modules/local/insilicoseq/generate/main.nf | 7 ++++++- nextflow.config | 1 + nextflow_schema.json | 11 +++++++++-- 3 files changed, 16 insertions(+), 3 deletions(-) diff --git a/modules/local/insilicoseq/generate/main.nf b/modules/local/insilicoseq/generate/main.nf index dbb1b41..0b8f08a 100644 --- a/modules/local/insilicoseq/generate/main.nf +++ b/modules/local/insilicoseq/generate/main.nf @@ -22,6 +22,11 @@ process INSILICOSEQ_GENERATE { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def seed = task.ext.seed ?: "${meta.seed}" + if ( params.metagenome_input_format == 'complete' ) { + def input_format '--genomes' + } if ( params.metagenome_input_format == 'draft' ) { + def input_format '--draft' + } if (fasta) { def is_compressed = fasta.name.endsWith(".gz") def fasta_name = fasta.name.replace(".gz", "") @@ -34,7 +39,7 @@ process INSILICOSEQ_GENERATE { fi iss generate \\ - --genomes ${fasta_name} \\ + ${input_format} ${fasta_name} \\ --seed \$seed \\ --output \$prefix \\ --compress \\ diff --git a/nextflow.config b/nextflow.config index 61105b2..29eccf3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -55,6 +55,7 @@ params { metagenome_abundance_file = null metagenome_coverage = null metagenome_coverage_file = null + metagenome_input_format = 'complete' metagenome_n_reads = '1M' metagenome_mode = 'kde' metagenome_model = 'MiSeq' diff --git a/nextflow_schema.json b/nextflow_schema.json index 90ffab0..f0cd80e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -158,7 +158,7 @@ }, "target_capture_fshape": { "type": "number", - "default": 6.0, + "default": 6, "description": "Shape parameter of the fragment size distribution." }, "target_capture_smedian": { @@ -168,7 +168,7 @@ }, "target_capture_sshape": { "type": "number", - "default": 6.0, + "default": 6, "description": "Shape parameter of the fragment size distribution." }, "target_capture_tmedian": { @@ -240,6 +240,13 @@ "description": "Path to tab-separated file containing coverage information.", "help_text": "The first column should contain the genome and the second column should contain the coverage (e.g., use the value 20 for a coverage of 20X)." }, + "metagenome_input_format": { + "type": "string", + "default": "complete", + "description": "Format of FASTA file used to generate reads", + "help_text": "If complete genomes are used (i.e. 1 sequence per genome FASTA) choose 'complete'; if draft genomes are used (i.e. multiple sequences per genome FASTA) choose 'draft'", + "enum": ["complete", "draft"] + }, "metagenome_n_reads": { "type": "string", "default": "1M", From 396a4022c2cb0009cefd3c79b9c903d1688fd43f Mon Sep 17 00:00:00 2001 From: Carson J Miller Date: Thu, 14 Mar 2024 14:47:39 +0000 Subject: [PATCH 04/40] Fixed syntax errors --- modules/local/insilicoseq/generate/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/insilicoseq/generate/main.nf b/modules/local/insilicoseq/generate/main.nf index 0b8f08a..fa05f9a 100644 --- a/modules/local/insilicoseq/generate/main.nf +++ b/modules/local/insilicoseq/generate/main.nf @@ -23,9 +23,9 @@ process INSILICOSEQ_GENERATE { def prefix = task.ext.prefix ?: "${meta.id}" def seed = task.ext.seed ?: "${meta.seed}" if ( params.metagenome_input_format == 'complete' ) { - def input_format '--genomes' - } if ( params.metagenome_input_format == 'draft' ) { - def input_format '--draft' + def input_format = '--genomes' + } else { + def input_format = '--draft' } if (fasta) { def is_compressed = fasta.name.endsWith(".gz") From d8595c49ce5053bcf76a24bd39211c06dee75a48 Mon Sep 17 00:00:00 2001 From: Carson J Miller Date: Thu, 14 Mar 2024 15:00:24 +0000 Subject: [PATCH 05/40] Fixed input_format variable --- modules/local/insilicoseq/generate/main.nf | 6 +----- nextflow.config | 2 +- nextflow_schema.json | 6 +++--- 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/modules/local/insilicoseq/generate/main.nf b/modules/local/insilicoseq/generate/main.nf index fa05f9a..db02183 100644 --- a/modules/local/insilicoseq/generate/main.nf +++ b/modules/local/insilicoseq/generate/main.nf @@ -22,11 +22,7 @@ process INSILICOSEQ_GENERATE { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def seed = task.ext.seed ?: "${meta.seed}" - if ( params.metagenome_input_format == 'complete' ) { - def input_format = '--genomes' - } else { - def input_format = '--draft' - } + def input_format = "--${params.metagenome_input_format}" if (fasta) { def is_compressed = fasta.name.endsWith(".gz") def fasta_name = fasta.name.replace(".gz", "") diff --git a/nextflow.config b/nextflow.config index 29eccf3..f1a292c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -55,7 +55,7 @@ params { metagenome_abundance_file = null metagenome_coverage = null metagenome_coverage_file = null - metagenome_input_format = 'complete' + metagenome_input_format = 'genomes' metagenome_n_reads = '1M' metagenome_mode = 'kde' metagenome_model = 'MiSeq' diff --git a/nextflow_schema.json b/nextflow_schema.json index f0cd80e..03f9fa8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -242,10 +242,10 @@ }, "metagenome_input_format": { "type": "string", - "default": "complete", + "default": "genomes", "description": "Format of FASTA file used to generate reads", - "help_text": "If complete genomes are used (i.e. 1 sequence per genome FASTA) choose 'complete'; if draft genomes are used (i.e. multiple sequences per genome FASTA) choose 'draft'", - "enum": ["complete", "draft"] + "help_text": "If complete genomes are used (i.e. 1 sequence per genome FASTA) choose 'genomes'; if draft genomes are used (i.e. multiple sequences per genome FASTA) choose 'draft'", + "enum": ["genomes", "draft"] }, "metagenome_n_reads": { "type": "string", From 71b4b57674dd0a60d32dcb9de92630c7de0ca4fb Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Fri, 15 Mar 2024 08:32:12 +0800 Subject: [PATCH 06/40] removed param from iss module --- modules/local/insilicoseq/generate/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/insilicoseq/generate/main.nf b/modules/local/insilicoseq/generate/main.nf index db02183..72ce205 100644 --- a/modules/local/insilicoseq/generate/main.nf +++ b/modules/local/insilicoseq/generate/main.nf @@ -9,6 +9,7 @@ process INSILICOSEQ_GENERATE { input: tuple val(meta), path(fasta) + val(input_format) output: tuple val(meta), path("*.fastq.gz*"), emit: fastq @@ -22,7 +23,7 @@ process INSILICOSEQ_GENERATE { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def seed = task.ext.seed ?: "${meta.seed}" - def input_format = "--${params.metagenome_input_format}" + def input_format = input_format == "genomes" ? "--genomes": "--draft" if (fasta) { def is_compressed = fasta.name.endsWith(".gz") def fasta_name = fasta.name.replace(".gz", "") From 38783b6884b477010defe40878f77f4d297dbbcd Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Fri, 15 Mar 2024 08:36:44 +0800 Subject: [PATCH 07/40] Update main.nf --- workflows/readsimulator/main.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index db38605..791a400 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -35,6 +35,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil // // MODULE: Local modules // +include { MERGE_FASTAS } from '../../modules/local/custom/merge_fastas/main' include { INSILICOSEQ_GENERATE } from '../../modules/local/insilicoseq/generate/main' // TODO: Add module to nf-core/modules include { CREATE_SAMPLESHEET } from '../../modules/local/custom/create_samplesheet/main' include { MERGE_SAMPLESHEETS } from '../../modules/local/custom/merge_samplesheets/main' @@ -149,7 +150,8 @@ workflow READSIMULATOR { // if ( params.metagenome ) { INSILICOSEQ_GENERATE ( - ch_input.combine(ch_fasta.ifEmpty([[]])) + ch_input.combine(ch_fasta.ifEmpty([[]])), + params.metagenome_input_format ) ch_versions = ch_versions.mix(INSILICOSEQ_GENERATE.out.versions.first()) ch_metagenome_reads = INSILICOSEQ_GENERATE.out.fastq From 9aa5de672ab0604def360855e28c5921b934d4f5 Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Fri, 15 Mar 2024 09:17:54 +0800 Subject: [PATCH 08/40] Update schema_input.json --- assets/schema_input.json | 20 ++++++-------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 33e4478..a2531cd 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -13,21 +13,13 @@ "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] }, - "fastq_1": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" - }, - "fastq_2": { - "type": "string", - "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + "seed": { + "type": "integer", + "errorMessage": "Seed must be provided", + "unique": true, + "meta": ["seed"] } }, - "required": ["sample", "fastq_1"] + "required": ["sample", "seed"] } } From 2f3b761df6053d8048b1f6787ed2e9e9ef29b43d Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Fri, 15 Mar 2024 09:24:45 +0800 Subject: [PATCH 09/40] remove fastq from samplesheet template update --- .../main.nf | 22 ++----------------- 1 file changed, 2 insertions(+), 20 deletions(-) diff --git a/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf index da28197..0e464af 100644 --- a/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf @@ -82,22 +82,10 @@ workflow PIPELINE_INITIALISATION { // Channel .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } .groupTuple() .map { validateInputSamplesheet(it) } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } .set { ch_samplesheet } emit: @@ -158,15 +146,9 @@ def validateInputParameters() { // Validate channels from input samplesheet // def validateInputSamplesheet(input) { - def (metas, fastqs) = input[1..2] - - // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 - if (!endedness_ok) { - error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") - } + def (metas, seeds) = input[1..2] - return [ metas[0], fastqs ] + return [ metas[0], seeds ] } // // Get attribute from genome config file e.g. fasta From ee274a805ff0c26ddef40972b17c3f57b43dd21e Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 01:46:03 +0000 Subject: [PATCH 10/40] added input to test profile --- conf/test.config | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/conf/test.config b/conf/test.config index d7b277f..e839fc0 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,10 +20,6 @@ params { max_time = '6.h' // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - // Genome references - genome = 'R64-1-1' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/samplesheet/test_samplesheet.csv' + fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/testdata/GCF_024334085.1_ASM2433408v1_genomic.fna.gz' } From 0d7fabded14fb2e749231c5ca5385fe1bb02e374 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 03:54:20 +0000 Subject: [PATCH 11/40] install nf-test in git workflow --- .github/workflows/ci.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1114bf1..60487be 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -80,6 +80,21 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Cache nf-test installation + id: cache-software + uses: actions/cache@v3 + with: + path: | + /usr/local/bin/nf-test + /home/runner/.nf-test/nf-test.jar + key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest + + - name: Install nf-test + if: steps.cache-software.outputs.cache-hit != 'true' + run: | + wget -qO- https://code.askimed.com/install/nf-test | bash + sudo mv nf-test /usr/local/bin/ + - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters From d84f76500e1d6f2f4b331bde5729ea34a5c3e979 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 04:20:01 +0000 Subject: [PATCH 12/40] merged new template changes with readsimulator main workflow --- workflows/readsimulator/main.nf | 112 +++++++++++--------------------- 1 file changed, 37 insertions(+), 75 deletions(-) diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index db38605..9e84072 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -1,63 +1,22 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowReadsimulator.initialise(params, log) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT LOCAL MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Local modules -// -include { INSILICOSEQ_GENERATE } from '../../modules/local/insilicoseq/generate/main' // TODO: Add module to nf-core/modules -include { CREATE_SAMPLESHEET } from '../../modules/local/custom/create_samplesheet/main' -include { MERGE_SAMPLESHEETS } from '../../modules/local/custom/merge_samplesheets/main' -include { WGSIM } from '../../modules/local/wgsim/main' // TODO: Add module to nf-core/modules - -// -// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules -// -include { AMPLICON_WORKFLOW } from '../../subworkflows/local/amplicon_workflow' -include { TARGET_CAPTURE_WORKFLOW } from '../../subworkflows/local/target_capture_workflow' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT NF-CORE MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Installed directly from nf-core/modules -// include { FASTQC } from '../../modules/nf-core/fastqc/main' -include { NCBIGENOMEDOWNLOAD } from '../../modules/nf-core/ncbigenomedownload/main' include { MULTIQC } from '../../modules/nf-core/multiqc/main' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_readsimulator_pipeline' +include { INSILICOSEQ_GENERATE } from '../../modules/local/insilicoseq/generate/main' // TODO: Add module to nf-core/modules +include { CREATE_SAMPLESHEET } from '../../modules/local/custom/create_samplesheet/main' +include { MERGE_SAMPLESHEETS } from '../../modules/local/custom/merge_samplesheets/main' +include { WGSIM } from '../../modules/local/wgsim/main' // TODO: Add module to nf-core/modules +include { AMPLICON_WORKFLOW } from '../../subworkflows/local/amplicon_workflow' +include { TARGET_CAPTURE_WORKFLOW } from '../../subworkflows/local/target_capture_workflow' +include { NCBIGENOMEDOWNLOAD } from '../../modules/nf-core/ncbigenomedownload/main' include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main' /* @@ -66,16 +25,15 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumps ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Info required for completion email and summary -def multiqc_report = [] - workflow READSIMULATOR { take: - ch_input + ch_samplesheet // channel: samplesheet read in from --input main: + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() ch_simulated_reads = Channel.empty() ch_taxids = Channel.empty() ch_accessions = Channel.empty() @@ -125,7 +83,7 @@ workflow READSIMULATOR { if ( params.amplicon ) { AMPLICON_WORKFLOW ( ch_fasta.ifEmpty([]), - ch_input + ch_samplesheet ) ch_versions = ch_versions.mix(AMPLICON_WORKFLOW.out.versions.first()) ch_simulated_reads = ch_simulated_reads.mix(AMPLICON_WORKFLOW.out.reads) @@ -137,7 +95,7 @@ workflow READSIMULATOR { if ( params.target_capture ) { TARGET_CAPTURE_WORKFLOW ( ch_fasta, - ch_input, + ch_samplesheet, ch_probes.ifEmpty([]) ) ch_versions = ch_versions.mix(TARGET_CAPTURE_WORKFLOW.out.versions.first()) @@ -149,7 +107,7 @@ workflow READSIMULATOR { // if ( params.metagenome ) { INSILICOSEQ_GENERATE ( - ch_input.combine(ch_fasta.ifEmpty([[]])) + ch_samplesheet.combine(ch_fasta.ifEmpty([[]])) ) ch_versions = ch_versions.mix(INSILICOSEQ_GENERATE.out.versions.first()) ch_metagenome_reads = INSILICOSEQ_GENERATE.out.fastq @@ -210,26 +168,29 @@ workflow READSIMULATOR { FASTQC ( ch_simulated_reads ) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + .set { ch_collated_versions } // // MODULE: MultiQC // - workflow_summary = WorkflowReadsimulator.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowReadsimulator.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) MULTIQC ( ch_multiqc_files.collect(), @@ -237,11 +198,12 @@ workflow READSIMULATOR { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - multiqc_report = MULTIQC.out.report.toList() emit: simulated_reads = ch_simulated_reads samplesheet = ch_final_samplesheet + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From 3f7bb2c7fb4a5cfa905a39f69224b0dabc6ef984 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 04:24:30 +0000 Subject: [PATCH 13/40] removed include customdumpsoftwareversion --- workflows/readsimulator/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index 9e84072..1f8a602 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -17,7 +17,6 @@ include { WGSIM } from '../../modules/local/wgsim/main' include { AMPLICON_WORKFLOW } from '../../subworkflows/local/amplicon_workflow' include { TARGET_CAPTURE_WORKFLOW } from '../../subworkflows/local/target_capture_workflow' include { NCBIGENOMEDOWNLOAD } from '../../modules/nf-core/ncbigenomedownload/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 6d004d376b51da9b99f42a2801233e13a9729152 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 04:43:01 +0000 Subject: [PATCH 14/40] change paths in nf-test tags --- workflows/readsimulator/tests/tags.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/readsimulator/tests/tags.yml b/workflows/readsimulator/tests/tags.yml index 393123b..b75960f 100644 --- a/workflows/readsimulator/tests/tags.yml +++ b/workflows/readsimulator/tests/tags.yml @@ -1,8 +1,8 @@ readsimulator_test_amplicon: - - ./** + - workflows/readsimulator/** readsimulator_test_wholegenome: - - ./** + - workflows/readsimulator/** readsimulator_test_metagenome: - - ./** + - workflows/readsimulator/** readsimulator_test_target_capture: - - ./** + - workflows/readsimulator/** From be16150f02145eae9880e16df3eaccbb7c5cc8ff Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 04:49:18 +0000 Subject: [PATCH 15/40] removed one more reference to ch_input --- workflows/readsimulator/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index 1f8a602..90954d2 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -124,7 +124,7 @@ workflow READSIMULATOR { // if ( params.wholegenome ) { WGSIM ( - ch_input.combine(ch_fasta) + ch_samplesheet.combine(ch_fasta) ) ch_versions = ch_versions.mix(WGSIM.out.versions.first()) ch_wholegenome_reads = WGSIM.out.fastq From 08d32140cd88e875396cb9ab2a06b4147ff6a8a0 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 05:10:37 +0000 Subject: [PATCH 16/40] changed nf-test snapshots to include chenges with template update --- workflows/readsimulator.nf | 76 ------------------- .../tests/test_amplicon.nf.test.snap | 20 ++++- .../tests/test_metagenome.nf.test.snap | 20 ++++- .../tests/test_target_capture.nf.test.snap | 20 ++++- .../tests/test_wholegenome.nf.test.snap | 18 +++++ 5 files changed, 75 insertions(+), 79 deletions(-) delete mode 100644 workflows/readsimulator.nf diff --git a/workflows/readsimulator.nf b/workflows/readsimulator.nf deleted file mode 100644 index 276dec0..0000000 --- a/workflows/readsimulator.nf +++ /dev/null @@ -1,76 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_readsimulator_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN MAIN WORKFLOW -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow READSIMULATOR { - - take: - ch_samplesheet // channel: samplesheet read in from --input - - main: - - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() - - // - // MODULE: Run FastQC - // - FASTQC ( - ch_samplesheet - ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - - // - // Collate and save software versions - // - softwareVersionsToYAML(ch_versions) - .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) - .set { ch_collated_versions } - - // - // MODULE: MultiQC - // - ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() - ) - - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html - versions = ch_versions // channel: [ path(versions.yml) ] -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test.snap b/workflows/readsimulator/tests/test_amplicon.nf.test.snap index 09f0d95..d802190 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test.snap +++ b/workflows/readsimulator/tests/test_amplicon.nf.test.snap @@ -48,6 +48,20 @@ "amplicon_illumina_samplesheet.csv:md5,2f0440b621dd2de3c89cda85c81e5be7" ] ], + "2": [ + [ + "multiqc_report.html:md5,b874c97a3d170cd7134f456b0f3c1453" + ] + ], + "3": [ + "versions.yml:md5,7282f5159b374e936cdb2a26261c07dd", + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" + ], + "multiqc_report": [ + [ + "multiqc_report.html:md5,b874c97a3d170cd7134f456b0f3c1453" + ] + ], "samplesheet": [ [ { @@ -93,9 +107,13 @@ "third2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] + ], + "versions": [ + "versions.yml:md5,7282f5159b374e936cdb2a26261c07dd", + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" ] } ], "timestamp": "2024-01-19T19:15:08.881730553" } -} \ No newline at end of file +} diff --git a/workflows/readsimulator/tests/test_metagenome.nf.test.snap b/workflows/readsimulator/tests/test_metagenome.nf.test.snap index a28510d..bc06292 100644 --- a/workflows/readsimulator/tests/test_metagenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_metagenome.nf.test.snap @@ -48,6 +48,20 @@ "metagenomic_illumina_samplesheet.csv:md5,8064936eff731e7c4c879916eb8b2edb" ] ], + "2": [ + [ + "multiqc_report.html:md5,bce82b348cebf13fdad80c9d1d1d1130" + ] + ], + "3": [ + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", + "versions.yml:md5,c8240bb3edb947511ec99bd2ef740b8a" + ], + "multiqc_report": [ + [ + "multiqc_report.html:md5,bce82b348cebf13fdad80c9d1d1d1130" + ] + ], "samplesheet": [ [ { @@ -93,9 +107,13 @@ "third_R2.fastq.gz:md5,3a78f893f1c12af70d13fe3df59eaa84" ] ] + ], + "versions": [ + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", + "versions.yml:md5,c8240bb3edb947511ec99bd2ef740b8a" ] } ], "timestamp": "2024-01-19T00:09:35.115953915" } -} \ No newline at end of file +} diff --git a/workflows/readsimulator/tests/test_target_capture.nf.test.snap b/workflows/readsimulator/tests/test_target_capture.nf.test.snap index f34ebaf..daddafe 100644 --- a/workflows/readsimulator/tests/test_target_capture.nf.test.snap +++ b/workflows/readsimulator/tests/test_target_capture.nf.test.snap @@ -48,6 +48,20 @@ "target_capture_samplesheet.csv:md5,5279e81ea6bcdee0e3d9e54f7cef1dab" ] ], + "2": [ + [ + "multiqc_report.html:md5,48162ab5564d48280542943b97fb0af3" + ] + ], + "3": [ + "versions.yml:md5,07f9a388a49fac3bf329410a1654fadd", + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" + ], + "multiqc_report": [ + [ + "multiqc_report.html:md5,48162ab5564d48280542943b97fb0af3" + ] + ], "samplesheet": [ [ { @@ -93,9 +107,13 @@ "third_2.fastq.gz:md5,995ea1c4eb2bcbb55b252dac290def09" ] ] + ], + "versions": [ + "versions.yml:md5,07f9a388a49fac3bf329410a1654fadd", + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" ] } ], "timestamp": "2024-01-19T00:15:17.918173096" } -} \ No newline at end of file +} diff --git a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap index 0d4e785..b05b633 100644 --- a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap @@ -48,6 +48,20 @@ "wholegenome_samplesheet.csv:md5,310b2ee2f03a2b44beb88da1816bc3d0" ] ], + "2": [ + [ + "multiqc_report.html:md5,917fc0076da11bc961b50786fb2f5f62" + ] + ], + "3": [ + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", + "versions.yml:md5,b59d45141b86b92640d12df20868c7b1" + ], + "multiqc_report": [ + [ + "multiqc_report.html:md5,917fc0076da11bc961b50786fb2f5f62" + ] + ], "samplesheet": [ [ { @@ -93,6 +107,10 @@ "third_R2.fq.gz:md5,e42714cc210d161fbb3df55c75e96d61" ] ] + ], + "versions": [ + "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", + "versions.yml:md5,b59d45141b86b92640d12df20868c7b1" ] } ], From bcca4ebf67c2adab7437e005ae90d3915a54b102 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 05:27:08 +0000 Subject: [PATCH 17/40] changed multiqc snapshot --- workflows/readsimulator/tests/test_amplicon.nf.test.snap | 4 ++-- workflows/readsimulator/tests/test_metagenome.nf.test.snap | 4 ++-- .../readsimulator/tests/test_target_capture.nf.test.snap | 4 ++-- workflows/readsimulator/tests/test_wholegenome.nf.test.snap | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test.snap b/workflows/readsimulator/tests/test_amplicon.nf.test.snap index d802190..c1f2b44 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test.snap +++ b/workflows/readsimulator/tests/test_amplicon.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,b874c97a3d170cd7134f456b0f3c1453" + "multiqc_report.html:md5,7275bee57bc698eb68d629faa9f0b77b" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,b874c97a3d170cd7134f456b0f3c1453" + "multiqc_report.html:md5,7275bee57bc698eb68d629faa9f0b77b" ] ], "samplesheet": [ diff --git a/workflows/readsimulator/tests/test_metagenome.nf.test.snap b/workflows/readsimulator/tests/test_metagenome.nf.test.snap index bc06292..596522c 100644 --- a/workflows/readsimulator/tests/test_metagenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_metagenome.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,bce82b348cebf13fdad80c9d1d1d1130" + "multiqc_report.html:md5,665f2220d3cce90eb5b7b901d8185549" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,bce82b348cebf13fdad80c9d1d1d1130" + "multiqc_report.html:md5,665f2220d3cce90eb5b7b901d8185549" ] ], "samplesheet": [ diff --git a/workflows/readsimulator/tests/test_target_capture.nf.test.snap b/workflows/readsimulator/tests/test_target_capture.nf.test.snap index daddafe..396032a 100644 --- a/workflows/readsimulator/tests/test_target_capture.nf.test.snap +++ b/workflows/readsimulator/tests/test_target_capture.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,48162ab5564d48280542943b97fb0af3" + "multiqc_report.html:md5,0398714a8adfe61cf4de7097365ccd3d" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,48162ab5564d48280542943b97fb0af3" + "multiqc_report.html:md5,0398714a8adfe61cf4de7097365ccd3d" ] ], "samplesheet": [ diff --git a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap index b05b633..0e18823 100644 --- a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,917fc0076da11bc961b50786fb2f5f62" + "multiqc_report.html:md5,a81f7fe0a54a9273a608a9bcd8d357fe" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,917fc0076da11bc961b50786fb2f5f62" + "multiqc_report.html:md5,a81f7fe0a54a9273a608a9bcd8d357fe" ] ], "samplesheet": [ From f44e82e999928d318f52d3c990edd43dba97a811 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 05:39:15 +0000 Subject: [PATCH 18/40] removed section that was removed with template change --- workflows/readsimulator/main.nf | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index 90954d2..8f6b870 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -205,30 +205,6 @@ workflow READSIMULATOR { versions = ch_versions // channel: [ path(versions.yml) ] } -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} - -workflow.onError { - if (workflow.errorReport.contains("Process requirement exceeds available memory")) { - println("🛑 Default resources exceed availability 🛑 ") - println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") - } -} - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END From 9a3fb9133ee18f6b0b35a0c811fa4521971f490a Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 06:37:26 +0000 Subject: [PATCH 19/40] resolved merge conflicts --- main.nf | 2 +- nextflow_schema.json | 1 - .../local/utils_nfcore_readsimulator_pipeline/main.nf | 4 +--- workflows/readsimulator/main.nf | 2 ++ 4 files changed, 4 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index b2a605f..40f3aca 100644 --- a/main.nf +++ b/main.nf @@ -33,7 +33,7 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_read // This is an example of how to use getGenomeAttribute() to fetch parameters // from igenomes.config using `--genome` if (!params.fasta) { - params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') + params.fasta = getGenomeAttribute('fasta') } /* diff --git a/nextflow_schema.json b/nextflow_schema.json index d4ce6c2..90ffab0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,7 +16,6 @@ "type": "string", "format": "file-path", "exists": true, - "schema": "assets/schema_input.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", diff --git a/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf index 0e464af..8c72a98 100644 --- a/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf @@ -146,9 +146,7 @@ def validateInputParameters() { // Validate channels from input samplesheet // def validateInputSamplesheet(input) { - def (metas, seeds) = input[1..2] - - return [ metas[0], seeds ] + return [ input[0] ] } // // Get attribute from genome config file e.g. fasta diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index 8f6b870..4e3dfb5 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -10,6 +10,7 @@ include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_readsimulator_pipeline' +include { MERGE_FASTAS } from '../../modules/local/custom/merge_fastas/main' include { INSILICOSEQ_GENERATE } from '../../modules/local/insilicoseq/generate/main' // TODO: Add module to nf-core/modules include { CREATE_SAMPLESHEET } from '../../modules/local/custom/create_samplesheet/main' include { MERGE_SAMPLESHEETS } from '../../modules/local/custom/merge_samplesheets/main' @@ -36,6 +37,7 @@ workflow READSIMULATOR { ch_simulated_reads = Channel.empty() ch_taxids = Channel.empty() ch_accessions = Channel.empty() + ch_fasta = Channel.empty() if ( params.fasta ) { ch_fasta = Channel.fromPath(params.fasta) From 926d28a0983fb7ad118bbb15c9eecd0c0bf76333 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 06:53:07 +0000 Subject: [PATCH 20/40] changing multiqc md5 --- workflows/readsimulator/tests/test_amplicon.nf.test.snap | 4 ++-- workflows/readsimulator/tests/test_metagenome.nf.test.snap | 4 ++-- .../readsimulator/tests/test_target_capture.nf.test.snap | 4 ++-- workflows/readsimulator/tests/test_wholegenome.nf.test.snap | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test.snap b/workflows/readsimulator/tests/test_amplicon.nf.test.snap index c1f2b44..b13bea0 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test.snap +++ b/workflows/readsimulator/tests/test_amplicon.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,7275bee57bc698eb68d629faa9f0b77b" + "multiqc_report.html:md5,eb157dddb3ba42fa225d303aa6c32364" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,7275bee57bc698eb68d629faa9f0b77b" + "multiqc_report.html:md5,eb157dddb3ba42fa225d303aa6c32364" ] ], "samplesheet": [ diff --git a/workflows/readsimulator/tests/test_metagenome.nf.test.snap b/workflows/readsimulator/tests/test_metagenome.nf.test.snap index 596522c..62c367f 100644 --- a/workflows/readsimulator/tests/test_metagenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_metagenome.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,665f2220d3cce90eb5b7b901d8185549" + "multiqc_report.html:md5,ebcfd57013f73d2afd52650543a88aee" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,665f2220d3cce90eb5b7b901d8185549" + "multiqc_report.html:md5,ebcfd57013f73d2afd52650543a88aee" ] ], "samplesheet": [ diff --git a/workflows/readsimulator/tests/test_target_capture.nf.test.snap b/workflows/readsimulator/tests/test_target_capture.nf.test.snap index 396032a..9e6fb9d 100644 --- a/workflows/readsimulator/tests/test_target_capture.nf.test.snap +++ b/workflows/readsimulator/tests/test_target_capture.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,0398714a8adfe61cf4de7097365ccd3d" + "multiqc_report.html:md5,e9a1edf0dcd702c777a4fff733213e28" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,0398714a8adfe61cf4de7097365ccd3d" + "multiqc_report.html:md5,e9a1edf0dcd702c777a4fff733213e28" ] ], "samplesheet": [ diff --git a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap index 0e18823..e674467 100644 --- a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,a81f7fe0a54a9273a608a9bcd8d357fe" + "multiqc_report.html:md5,ffa56666596c609eed29e0fa47ebba41" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,a81f7fe0a54a9273a608a9bcd8d357fe" + "multiqc_report.html:md5,ffa56666596c609eed29e0fa47ebba41" ] ], "samplesheet": [ From e9c44bf99878c379fbcc7014974545f317ab230f Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 06:59:06 +0000 Subject: [PATCH 21/40] adding outdir to amplicon test --- workflows/readsimulator/tests/test_amplicon.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test b/workflows/readsimulator/tests/test_amplicon.nf.test index 3eccfd0..75ac4aa 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test +++ b/workflows/readsimulator/tests/test_amplicon.nf.test @@ -26,6 +26,7 @@ nextflow_workflow { amplicon_read_count = 1000 amplicon_crabs_ispcr_error = 0 fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/testdata/GCF_024334085.1_ASM2433408v1_genomic.fna.gz' + outdir = "results" } } From 4f82fe986228ac7a85df38001c44a1aff1265c2a Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 07:07:17 +0000 Subject: [PATCH 22/40] added outdir to other tests --- workflows/readsimulator/tests/test_amplicon.nf.test.snap | 4 ++-- workflows/readsimulator/tests/test_metagenome.nf.test | 1 + workflows/readsimulator/tests/test_target_capture.nf.test | 1 + workflows/readsimulator/tests/test_wholegenome.nf.test | 1 + 4 files changed, 5 insertions(+), 2 deletions(-) diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test.snap b/workflows/readsimulator/tests/test_amplicon.nf.test.snap index b13bea0..e2d6739 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test.snap +++ b/workflows/readsimulator/tests/test_amplicon.nf.test.snap @@ -50,7 +50,7 @@ ], "2": [ [ - "multiqc_report.html:md5,eb157dddb3ba42fa225d303aa6c32364" + "multiqc_report.html:md5,788578636e6f53ba65a66cecf8172f3a" ] ], "3": [ @@ -59,7 +59,7 @@ ], "multiqc_report": [ [ - "multiqc_report.html:md5,eb157dddb3ba42fa225d303aa6c32364" + "multiqc_report.html:md5,788578636e6f53ba65a66cecf8172f3a" ] ], "samplesheet": [ diff --git a/workflows/readsimulator/tests/test_metagenome.nf.test b/workflows/readsimulator/tests/test_metagenome.nf.test index ee53e2d..30903f3 100644 --- a/workflows/readsimulator/tests/test_metagenome.nf.test +++ b/workflows/readsimulator/tests/test_metagenome.nf.test @@ -23,6 +23,7 @@ nextflow_workflow { metagenome = true metagenome_n_reads = '100K' fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/testdata/GCF_024334085.1_ASM2433408v1_genomic.fna.gz' + outdir = "results" } } diff --git a/workflows/readsimulator/tests/test_target_capture.nf.test b/workflows/readsimulator/tests/test_target_capture.nf.test index ef73254..8f47a0b 100644 --- a/workflows/readsimulator/tests/test_target_capture.nf.test +++ b/workflows/readsimulator/tests/test_target_capture.nf.test @@ -23,6 +23,7 @@ nextflow_workflow { target_capture = true probe_ref_name = 'Diptera-2.7Kv1' fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/testdata/GCF_024334085.1_ASM2433408v1_genomic.fna.gz' + outdir = "results" } } diff --git a/workflows/readsimulator/tests/test_wholegenome.nf.test b/workflows/readsimulator/tests/test_wholegenome.nf.test index 1ad3498..98516e5 100644 --- a/workflows/readsimulator/tests/test_wholegenome.nf.test +++ b/workflows/readsimulator/tests/test_wholegenome.nf.test @@ -22,6 +22,7 @@ nextflow_workflow { params { wholegenome = true fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/testdata/GCF_024334085.1_ASM2433408v1_genomic.fna.gz' + outdir = "results" } } From 2aedae2b233c86478ec57c6677be78f6663b9542 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 15 Mar 2024 07:16:32 +0000 Subject: [PATCH 23/40] fixed parameter names in amplicon test --- workflows/readsimulator/tests/test_amplicon.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test b/workflows/readsimulator/tests/test_amplicon.nf.test index 75ac4aa..de47e11 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test +++ b/workflows/readsimulator/tests/test_amplicon.nf.test @@ -21,8 +21,8 @@ nextflow_workflow { } params { amplicon = true - fw_primer = 'AAAATAAT' - rv_primer = 'GATTACTTT' + amplicon_fw_primer = 'AAAATAAT' + amplicon_rv_primer = 'GATTACTTT' amplicon_read_count = 1000 amplicon_crabs_ispcr_error = 0 fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/testdata/GCF_024334085.1_ASM2433408v1_genomic.fna.gz' From a4425545f9f42bee4ee47ff303ebb5fc1bfa925e Mon Sep 17 00:00:00 2001 From: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> Date: Tue, 19 Mar 2024 15:06:27 +0000 Subject: [PATCH 24/40] Updated workflow tests to exclude multiqc_report --- .../readsimulator/tests/test_amplicon.nf.test | 2 +- .../tests/test_amplicon.nf.test.snap | 146 +++++------------- .../tests/test_metagenome.nf.test | 2 +- .../tests/test_metagenome.nf.test.snap | 146 +++++------------- .../tests/test_target_capture.nf.test | 2 +- .../tests/test_target_capture.nf.test.snap | 146 +++++------------- .../tests/test_wholegenome.nf.test | 2 +- .../tests/test_wholegenome.nf.test.snap | 146 +++++------------- 8 files changed, 156 insertions(+), 436 deletions(-) diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test b/workflows/readsimulator/tests/test_amplicon.nf.test index de47e11..0395e9d 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test +++ b/workflows/readsimulator/tests/test_amplicon.nf.test @@ -34,7 +34,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out + workflow.out.get(0).findAll { it != "multiqc_report" } ).match() } ) } diff --git a/workflows/readsimulator/tests/test_amplicon.nf.test.snap b/workflows/readsimulator/tests/test_amplicon.nf.test.snap index e2d6739..862cf1b 100644 --- a/workflows/readsimulator/tests/test_amplicon.nf.test.snap +++ b/workflows/readsimulator/tests/test_amplicon.nf.test.snap @@ -1,119 +1,49 @@ { "amplicon = true": { "content": [ - { - "0": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "art_illumina", - "datatype": "amplicon_illumina" - }, - [ - "first1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "first2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "art_illumina", - "datatype": "amplicon_illumina" - }, - [ - "second1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "second2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "art_illumina", - "datatype": "amplicon_illumina" - }, - [ - "third1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "third2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "1": [ - [ - { - "id": "amplicon_illumina" - }, - "amplicon_illumina_samplesheet.csv:md5,2f0440b621dd2de3c89cda85c81e5be7" - ] - ], - "2": [ - [ - "multiqc_report.html:md5,788578636e6f53ba65a66cecf8172f3a" + [ + [ + { + "id": "first", + "seed": 40, + "outdir": "art_illumina", + "datatype": "amplicon_illumina" + }, + [ + "first1.fq.gz:md5,5dfb2de5a3d547b4a1cbdfe8fe33eb78", + "first2.fq.gz:md5,3ff099ec08c9d1f1f87f7bcd1455aad3" ] ], - "3": [ - "versions.yml:md5,7282f5159b374e936cdb2a26261c07dd", - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" - ], - "multiqc_report": [ - [ - "multiqc_report.html:md5,788578636e6f53ba65a66cecf8172f3a" + [ + { + "id": "second", + "seed": 41, + "outdir": "art_illumina", + "datatype": "amplicon_illumina" + }, + [ + "second1.fq.gz:md5,fdb32a77b5d100efd77f9b253475b354", + "second2.fq.gz:md5,97b1101a3a2a3814f301ccd90b5c2f30" ] ], - "samplesheet": [ - [ - { - "id": "amplicon_illumina" - }, - "amplicon_illumina_samplesheet.csv:md5,2f0440b621dd2de3c89cda85c81e5be7" + [ + { + "id": "third", + "seed": 42, + "outdir": "art_illumina", + "datatype": "amplicon_illumina" + }, + [ + "third1.fq.gz:md5,62ab3b38160c81c9d9fa972871f896d3", + "third2.fq.gz:md5,912ae27dc22fea5b3d2f8f3a5dd4fa08" ] - ], - "simulated_reads": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "art_illumina", - "datatype": "amplicon_illumina" - }, - [ - "first1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "first2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "art_illumina", - "datatype": "amplicon_illumina" - }, - [ - "second1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "second2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "art_illumina", - "datatype": "amplicon_illumina" - }, - [ - "third1.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "third2.fq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions": [ - "versions.yml:md5,7282f5159b374e936cdb2a26261c07dd", - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" ] - } + ] ], - "timestamp": "2024-01-19T19:15:08.881730553" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T14:38:49.385639018" } -} +} \ No newline at end of file diff --git a/workflows/readsimulator/tests/test_metagenome.nf.test b/workflows/readsimulator/tests/test_metagenome.nf.test index 30903f3..91eed54 100644 --- a/workflows/readsimulator/tests/test_metagenome.nf.test +++ b/workflows/readsimulator/tests/test_metagenome.nf.test @@ -31,7 +31,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out + workflow.out.get(0).findAll { it != "multiqc_report" } ).match() } ) } diff --git a/workflows/readsimulator/tests/test_metagenome.nf.test.snap b/workflows/readsimulator/tests/test_metagenome.nf.test.snap index 62c367f..d70ee76 100644 --- a/workflows/readsimulator/tests/test_metagenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_metagenome.nf.test.snap @@ -1,119 +1,49 @@ { "metagenome = true": { "content": [ - { - "0": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "insilicoseq", - "datatype": "metagenomic_illumina" - }, - [ - "first_R1.fastq.gz:md5,2a324062e0afb4d3eab8134479f317d4", - "first_R2.fastq.gz:md5,9e0c86c0ff15091734fe7d52039f7727" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "insilicoseq", - "datatype": "metagenomic_illumina" - }, - [ - "second_R1.fastq.gz:md5,3536190205e1a6ba3609fe6a1567e0c7", - "second_R2.fastq.gz:md5,a91ff7cf5ea2069d541fc7d081c82bfb" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "insilicoseq", - "datatype": "metagenomic_illumina" - }, - [ - "third_R1.fastq.gz:md5,137d1f3ced4783a0a45f6d7aed6da743", - "third_R2.fastq.gz:md5,3a78f893f1c12af70d13fe3df59eaa84" - ] - ] - ], - "1": [ - [ - { - "id": "metagenomic_illumina" - }, - "metagenomic_illumina_samplesheet.csv:md5,8064936eff731e7c4c879916eb8b2edb" - ] - ], - "2": [ - [ - "multiqc_report.html:md5,ebcfd57013f73d2afd52650543a88aee" + [ + [ + { + "id": "first", + "seed": 40, + "outdir": "insilicoseq", + "datatype": "metagenomic_illumina" + }, + [ + "first_R1.fastq.gz:md5,2a324062e0afb4d3eab8134479f317d4", + "first_R2.fastq.gz:md5,9e0c86c0ff15091734fe7d52039f7727" ] ], - "3": [ - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", - "versions.yml:md5,c8240bb3edb947511ec99bd2ef740b8a" - ], - "multiqc_report": [ - [ - "multiqc_report.html:md5,ebcfd57013f73d2afd52650543a88aee" + [ + { + "id": "second", + "seed": 41, + "outdir": "insilicoseq", + "datatype": "metagenomic_illumina" + }, + [ + "second_R1.fastq.gz:md5,3536190205e1a6ba3609fe6a1567e0c7", + "second_R2.fastq.gz:md5,a91ff7cf5ea2069d541fc7d081c82bfb" ] ], - "samplesheet": [ - [ - { - "id": "metagenomic_illumina" - }, - "metagenomic_illumina_samplesheet.csv:md5,8064936eff731e7c4c879916eb8b2edb" + [ + { + "id": "third", + "seed": 42, + "outdir": "insilicoseq", + "datatype": "metagenomic_illumina" + }, + [ + "third_R1.fastq.gz:md5,137d1f3ced4783a0a45f6d7aed6da743", + "third_R2.fastq.gz:md5,3a78f893f1c12af70d13fe3df59eaa84" ] - ], - "simulated_reads": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "insilicoseq", - "datatype": "metagenomic_illumina" - }, - [ - "first_R1.fastq.gz:md5,2a324062e0afb4d3eab8134479f317d4", - "first_R2.fastq.gz:md5,9e0c86c0ff15091734fe7d52039f7727" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "insilicoseq", - "datatype": "metagenomic_illumina" - }, - [ - "second_R1.fastq.gz:md5,3536190205e1a6ba3609fe6a1567e0c7", - "second_R2.fastq.gz:md5,a91ff7cf5ea2069d541fc7d081c82bfb" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "insilicoseq", - "datatype": "metagenomic_illumina" - }, - [ - "third_R1.fastq.gz:md5,137d1f3ced4783a0a45f6d7aed6da743", - "third_R2.fastq.gz:md5,3a78f893f1c12af70d13fe3df59eaa84" - ] - ] - ], - "versions": [ - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", - "versions.yml:md5,c8240bb3edb947511ec99bd2ef740b8a" ] - } + ] ], - "timestamp": "2024-01-19T00:09:35.115953915" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T14:51:11.751345459" } -} +} \ No newline at end of file diff --git a/workflows/readsimulator/tests/test_target_capture.nf.test b/workflows/readsimulator/tests/test_target_capture.nf.test index 8f47a0b..e83f8b7 100644 --- a/workflows/readsimulator/tests/test_target_capture.nf.test +++ b/workflows/readsimulator/tests/test_target_capture.nf.test @@ -31,7 +31,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out + workflow.out.get(0).findAll { it != "multiqc_report" } ).match() } ) } diff --git a/workflows/readsimulator/tests/test_target_capture.nf.test.snap b/workflows/readsimulator/tests/test_target_capture.nf.test.snap index 9e6fb9d..fba6689 100644 --- a/workflows/readsimulator/tests/test_target_capture.nf.test.snap +++ b/workflows/readsimulator/tests/test_target_capture.nf.test.snap @@ -1,119 +1,49 @@ { "target_capture = true": { "content": [ - { - "0": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "capsim", - "datatype": "target_capture" - }, - [ - "first_1.fastq.gz:md5,a0d28da7897cdce5380fd803ca43fbd8", - "first_2.fastq.gz:md5,4b72a945f433797a05635996d7e41bdf" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "capsim", - "datatype": "target_capture" - }, - [ - "second_1.fastq.gz:md5,3cb9456d6373288c877eb59ef01cb4b1", - "second_2.fastq.gz:md5,c5d09485a7b3dffba13fd5f8c827c498" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "capsim", - "datatype": "target_capture" - }, - [ - "third_1.fastq.gz:md5,b7d11fb1d6fe768d17ee9940ed90d03c", - "third_2.fastq.gz:md5,995ea1c4eb2bcbb55b252dac290def09" - ] - ] - ], - "1": [ - [ - { - "id": "target_capture" - }, - "target_capture_samplesheet.csv:md5,5279e81ea6bcdee0e3d9e54f7cef1dab" - ] - ], - "2": [ - [ - "multiqc_report.html:md5,e9a1edf0dcd702c777a4fff733213e28" + [ + [ + { + "id": "first", + "seed": 40, + "outdir": "capsim", + "datatype": "target_capture" + }, + [ + "first_1.fastq.gz:md5,a0d28da7897cdce5380fd803ca43fbd8", + "first_2.fastq.gz:md5,4b72a945f433797a05635996d7e41bdf" ] ], - "3": [ - "versions.yml:md5,07f9a388a49fac3bf329410a1654fadd", - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" - ], - "multiqc_report": [ - [ - "multiqc_report.html:md5,e9a1edf0dcd702c777a4fff733213e28" + [ + { + "id": "second", + "seed": 41, + "outdir": "capsim", + "datatype": "target_capture" + }, + [ + "second_1.fastq.gz:md5,3cb9456d6373288c877eb59ef01cb4b1", + "second_2.fastq.gz:md5,c5d09485a7b3dffba13fd5f8c827c498" ] ], - "samplesheet": [ - [ - { - "id": "target_capture" - }, - "target_capture_samplesheet.csv:md5,5279e81ea6bcdee0e3d9e54f7cef1dab" + [ + { + "id": "third", + "seed": 42, + "outdir": "capsim", + "datatype": "target_capture" + }, + [ + "third_1.fastq.gz:md5,b7d11fb1d6fe768d17ee9940ed90d03c", + "third_2.fastq.gz:md5,995ea1c4eb2bcbb55b252dac290def09" ] - ], - "simulated_reads": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "capsim", - "datatype": "target_capture" - }, - [ - "first_1.fastq.gz:md5,a0d28da7897cdce5380fd803ca43fbd8", - "first_2.fastq.gz:md5,4b72a945f433797a05635996d7e41bdf" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "capsim", - "datatype": "target_capture" - }, - [ - "second_1.fastq.gz:md5,3cb9456d6373288c877eb59ef01cb4b1", - "second_2.fastq.gz:md5,c5d09485a7b3dffba13fd5f8c827c498" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "capsim", - "datatype": "target_capture" - }, - [ - "third_1.fastq.gz:md5,b7d11fb1d6fe768d17ee9940ed90d03c", - "third_2.fastq.gz:md5,995ea1c4eb2bcbb55b252dac290def09" - ] - ] - ], - "versions": [ - "versions.yml:md5,07f9a388a49fac3bf329410a1654fadd", - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c" ] - } + ] ], - "timestamp": "2024-01-19T00:15:17.918173096" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T15:01:05.767948266" } -} +} \ No newline at end of file diff --git a/workflows/readsimulator/tests/test_wholegenome.nf.test b/workflows/readsimulator/tests/test_wholegenome.nf.test index 98516e5..741b80a 100644 --- a/workflows/readsimulator/tests/test_wholegenome.nf.test +++ b/workflows/readsimulator/tests/test_wholegenome.nf.test @@ -30,7 +30,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out + workflow.out.get(0).findAll { it != "multiqc_report" } ).match() } ) } diff --git a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap index e674467..d816d0e 100644 --- a/workflows/readsimulator/tests/test_wholegenome.nf.test.snap +++ b/workflows/readsimulator/tests/test_wholegenome.nf.test.snap @@ -1,119 +1,49 @@ { "wholegenome = true": { "content": [ - { - "0": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "wgsim", - "datatype": "wholegenome" - }, - [ - "first_R1.fq.gz:md5,90ebdcc4f7783290afe3e6ee02d6d803", - "first_R2.fq.gz:md5,bfb972c268a36edcef29317fd1ced544" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "wgsim", - "datatype": "wholegenome" - }, - [ - "second_R1.fq.gz:md5,7902aa5c9041fc9e2585ebdd0c83597e", - "second_R2.fq.gz:md5,fa9f52716714e16d354e575c331d4ffc" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "wgsim", - "datatype": "wholegenome" - }, - [ - "third_R1.fq.gz:md5,a76e6d7ab7a4f4bae18747ae6abb607e", - "third_R2.fq.gz:md5,e42714cc210d161fbb3df55c75e96d61" - ] - ] - ], - "1": [ - [ - { - "id": "wholegenome" - }, - "wholegenome_samplesheet.csv:md5,310b2ee2f03a2b44beb88da1816bc3d0" - ] - ], - "2": [ - [ - "multiqc_report.html:md5,ffa56666596c609eed29e0fa47ebba41" + [ + [ + { + "id": "first", + "seed": 40, + "outdir": "wgsim", + "datatype": "wholegenome" + }, + [ + "first_R1.fq.gz:md5,90ebdcc4f7783290afe3e6ee02d6d803", + "first_R2.fq.gz:md5,bfb972c268a36edcef29317fd1ced544" ] ], - "3": [ - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", - "versions.yml:md5,b59d45141b86b92640d12df20868c7b1" - ], - "multiqc_report": [ - [ - "multiqc_report.html:md5,ffa56666596c609eed29e0fa47ebba41" + [ + { + "id": "second", + "seed": 41, + "outdir": "wgsim", + "datatype": "wholegenome" + }, + [ + "second_R1.fq.gz:md5,7902aa5c9041fc9e2585ebdd0c83597e", + "second_R2.fq.gz:md5,fa9f52716714e16d354e575c331d4ffc" ] ], - "samplesheet": [ - [ - { - "id": "wholegenome" - }, - "wholegenome_samplesheet.csv:md5,310b2ee2f03a2b44beb88da1816bc3d0" + [ + { + "id": "third", + "seed": 42, + "outdir": "wgsim", + "datatype": "wholegenome" + }, + [ + "third_R1.fq.gz:md5,a76e6d7ab7a4f4bae18747ae6abb607e", + "third_R2.fq.gz:md5,e42714cc210d161fbb3df55c75e96d61" ] - ], - "simulated_reads": [ - [ - { - "id": "first", - "seed": 40, - "outdir": "wgsim", - "datatype": "wholegenome" - }, - [ - "first_R1.fq.gz:md5,90ebdcc4f7783290afe3e6ee02d6d803", - "first_R2.fq.gz:md5,bfb972c268a36edcef29317fd1ced544" - ] - ], - [ - { - "id": "second", - "seed": 41, - "outdir": "wgsim", - "datatype": "wholegenome" - }, - [ - "second_R1.fq.gz:md5,7902aa5c9041fc9e2585ebdd0c83597e", - "second_R2.fq.gz:md5,fa9f52716714e16d354e575c331d4ffc" - ] - ], - [ - { - "id": "third", - "seed": 42, - "outdir": "wgsim", - "datatype": "wholegenome" - }, - [ - "third_R1.fq.gz:md5,a76e6d7ab7a4f4bae18747ae6abb607e", - "third_R2.fq.gz:md5,e42714cc210d161fbb3df55c75e96d61" - ] - ] - ], - "versions": [ - "versions.yml:md5,8acb8b7e1c904e2100c4a4451a880d9c", - "versions.yml:md5,b59d45141b86b92640d12df20868c7b1" ] - } + ] ], - "timestamp": "2024-01-19T00:04:12.073328968" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T15:05:42.660779239" } -} +} \ No newline at end of file From b57d2fa1e7216d94c438c4d9de7cc5b9a3420279 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Wed, 20 Mar 2024 08:53:33 +0800 Subject: [PATCH 25/40] resolve some conflicts with template update --- README.md | 9 +- workflows/readsimulator/main.nf | 143 +++++++++----------------------- 2 files changed, 45 insertions(+), 107 deletions(-) diff --git a/README.md b/README.md index ecd9a11..47be1a9 100644 --- a/README.md +++ b/README.md @@ -5,14 +5,15 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/readsimulator/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/readsimulator/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/readsimulator/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/readsimulator/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/readsimulator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10622410-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10622410) +[![GitHub Actions CI Status](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/readsimulator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10622410-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10622410) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/readsimulator) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/readsimulator) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23readsimulator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/readsimulator)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) @@ -112,7 +113,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use nf-core/readsimulator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.10622410) +If you use nf-core/readsimulator for your analysis, please cite it using the following doi: [10.5281/zenodo.10622410](https://doi.org/10.5281/zenodo.10622410) diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index 791a400..4e3dfb5 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -1,65 +1,23 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowReadsimulator.initialise(params, log) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT LOCAL MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Local modules -// -include { MERGE_FASTAS } from '../../modules/local/custom/merge_fastas/main' -include { INSILICOSEQ_GENERATE } from '../../modules/local/insilicoseq/generate/main' // TODO: Add module to nf-core/modules -include { CREATE_SAMPLESHEET } from '../../modules/local/custom/create_samplesheet/main' -include { MERGE_SAMPLESHEETS } from '../../modules/local/custom/merge_samplesheets/main' -include { WGSIM } from '../../modules/local/wgsim/main' // TODO: Add module to nf-core/modules - -// -// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules -// -include { AMPLICON_WORKFLOW } from '../../subworkflows/local/amplicon_workflow' -include { TARGET_CAPTURE_WORKFLOW } from '../../subworkflows/local/target_capture_workflow' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT NF-CORE MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Installed directly from nf-core/modules -// include { FASTQC } from '../../modules/nf-core/fastqc/main' -include { NCBIGENOMEDOWNLOAD } from '../../modules/nf-core/ncbigenomedownload/main' include { MULTIQC } from '../../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_readsimulator_pipeline' +include { MERGE_FASTAS } from '../../modules/local/custom/merge_fastas/main' +include { INSILICOSEQ_GENERATE } from '../../modules/local/insilicoseq/generate/main' // TODO: Add module to nf-core/modules +include { CREATE_SAMPLESHEET } from '../../modules/local/custom/create_samplesheet/main' +include { MERGE_SAMPLESHEETS } from '../../modules/local/custom/merge_samplesheets/main' +include { WGSIM } from '../../modules/local/wgsim/main' // TODO: Add module to nf-core/modules +include { AMPLICON_WORKFLOW } from '../../subworkflows/local/amplicon_workflow' +include { TARGET_CAPTURE_WORKFLOW } from '../../subworkflows/local/target_capture_workflow' +include { NCBIGENOMEDOWNLOAD } from '../../modules/nf-core/ncbigenomedownload/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -67,19 +25,19 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumps ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Info required for completion email and summary -def multiqc_report = [] - workflow READSIMULATOR { take: - ch_input + ch_samplesheet // channel: samplesheet read in from --input main: + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() ch_simulated_reads = Channel.empty() ch_taxids = Channel.empty() ch_accessions = Channel.empty() + ch_fasta = Channel.empty() if ( params.fasta ) { ch_fasta = Channel.fromPath(params.fasta) @@ -126,7 +84,7 @@ workflow READSIMULATOR { if ( params.amplicon ) { AMPLICON_WORKFLOW ( ch_fasta.ifEmpty([]), - ch_input + ch_samplesheet ) ch_versions = ch_versions.mix(AMPLICON_WORKFLOW.out.versions.first()) ch_simulated_reads = ch_simulated_reads.mix(AMPLICON_WORKFLOW.out.reads) @@ -138,7 +96,7 @@ workflow READSIMULATOR { if ( params.target_capture ) { TARGET_CAPTURE_WORKFLOW ( ch_fasta, - ch_input, + ch_samplesheet, ch_probes.ifEmpty([]) ) ch_versions = ch_versions.mix(TARGET_CAPTURE_WORKFLOW.out.versions.first()) @@ -150,8 +108,7 @@ workflow READSIMULATOR { // if ( params.metagenome ) { INSILICOSEQ_GENERATE ( - ch_input.combine(ch_fasta.ifEmpty([[]])), - params.metagenome_input_format + ch_samplesheet.combine(ch_fasta.ifEmpty([[]])) ) ch_versions = ch_versions.mix(INSILICOSEQ_GENERATE.out.versions.first()) ch_metagenome_reads = INSILICOSEQ_GENERATE.out.fastq @@ -169,7 +126,7 @@ workflow READSIMULATOR { // if ( params.wholegenome ) { WGSIM ( - ch_input.combine(ch_fasta) + ch_samplesheet.combine(ch_fasta) ) ch_versions = ch_versions.mix(WGSIM.out.versions.first()) ch_wholegenome_reads = WGSIM.out.fastq @@ -212,26 +169,29 @@ workflow READSIMULATOR { FASTQC ( ch_simulated_reads ) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + .set { ch_collated_versions } // // MODULE: MultiQC // - workflow_summary = WorkflowReadsimulator.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowReadsimulator.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) MULTIQC ( ch_multiqc_files.collect(), @@ -239,35 +199,12 @@ workflow READSIMULATOR { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - multiqc_report = MULTIQC.out.report.toList() emit: simulated_reads = ch_simulated_reads samplesheet = ch_final_samplesheet -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} - -workflow.onError { - if (workflow.errorReport.contains("Process requirement exceeds available memory")) { - println("🛑 Default resources exceed availability 🛑 ") - println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") - } + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From bd8a7c5f43a5d0142291c067dc27aaf3f2ed0439 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 22 Mar 2024 09:17:58 +0800 Subject: [PATCH 26/40] modified changelog for minor release --- CHANGELOG.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e76994e..0829673 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.0.1 - 2024-03-22 + +Minor release after nf-core template 2.13.1 update + +### `Added` + +- Merged nf-core template 2.13.1 update + +### `Fixed` + +- Fixed metagenome mode to allow draft genomes + ## v1.0.0 - 2024-02-07 Initial release of nf-core/readsimulator, created with the [nf-core](https://nf-co.re/) template. From 50c36f5a5d6c839ef017e23261932b54df6be5a9 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 22 Mar 2024 01:49:13 +0000 Subject: [PATCH 27/40] Bumped version to 1.0.1 --- CHANGELOG.md | 4 ++-- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0829673..4642502 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.1 - 2024-03-22 +## 1.0.1 - 2024-03-22 Minor release after nf-core template 2.13.1 update @@ -15,7 +15,7 @@ Minor release after nf-core template 2.13.1 update - Fixed metagenome mode to allow draft genomes -## v1.0.0 - 2024-02-07 +## 1.0.0 - 2024-02-07 Initial release of nf-core/readsimulator, created with the [nf-core](https://nf-co.re/) template. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 142d822..b50a5fc 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,8 +1,8 @@ report_comment: > - This report has been generated by the nf-core/readsimulator + This report has been generated by the nf-core/readsimulator analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-readsimulator-methods-description": diff --git a/nextflow.config b/nextflow.config index 797fc63..ad77ce8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -290,7 +290,7 @@ manifest { description = """A workflow to simulate reads""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.0.0' + version = '1.0.1' doi = '10.5281/zenodo.10622410' } From d7c633181a56a6963207ecd55f6f4e53a3da4eaa Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Tue, 26 Mar 2024 07:32:31 +0800 Subject: [PATCH 28/40] modified changelog with decription of a bug that was fixed --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4642502..5eb55f0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ Minor release after nf-core template 2.13.1 update ### `Fixed` - Fixed metagenome mode to allow draft genomes +- Fixed bug with MERGE_FASTA process not being declared ## 1.0.0 - 2024-02-07 From eafa6e0289c5f3bb74da79cfb490e1be6a0b57bb Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Tue, 26 Mar 2024 08:12:51 +0800 Subject: [PATCH 29/40] Added PR numbers to changelog --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5eb55f0..2cb4f5e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,12 +9,12 @@ Minor release after nf-core template 2.13.1 update ### `Added` -- Merged nf-core template 2.13.1 update +- [#36] - Merged nf-core template 2.13.1 update ### `Fixed` -- Fixed metagenome mode to allow draft genomes -- Fixed bug with MERGE_FASTA process not being declared +- [#38] - Fixed metagenome mode to allow draft genomes +- [#36] - Fixed bug with MERGE_FASTA process not being declared ## 1.0.0 - 2024-02-07 From a6e666b46ac53f831cc45363e0183371fa0afc0c Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Tue, 26 Mar 2024 09:30:25 +0800 Subject: [PATCH 30/40] Added params.metagenome_input_format that is needed for INSILICOSEQ_GENERATE --- workflows/readsimulator/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/readsimulator/main.nf b/workflows/readsimulator/main.nf index 4e3dfb5..e8b421a 100644 --- a/workflows/readsimulator/main.nf +++ b/workflows/readsimulator/main.nf @@ -108,7 +108,8 @@ workflow READSIMULATOR { // if ( params.metagenome ) { INSILICOSEQ_GENERATE ( - ch_samplesheet.combine(ch_fasta.ifEmpty([[]])) + ch_samplesheet.combine(ch_fasta.ifEmpty([[]])), + params.metagenome_input_format ) ch_versions = ch_versions.mix(INSILICOSEQ_GENERATE.out.versions.first()) ch_metagenome_reads = INSILICOSEQ_GENERATE.out.fastq From db895f72837345608f2a7c9fc8c14037349ed0d8 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Wed, 27 Mar 2024 07:57:52 +0800 Subject: [PATCH 31/40] added input parameter to pipeline download --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 08622fd..6ff33f0 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -69,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results --input https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/samplesheet/test_samplesheet.csv From f42fb596f8d14471ae77c38da74508a3e5597c83 Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Tue, 2 Apr 2024 08:12:40 +0800 Subject: [PATCH 32/40] Removed -stub option from download_pipeline.yml command --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 6ff33f0..48fe5d0 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -69,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results --input https://raw.githubusercontent.com/nf-core/test-datasets/readsimulator/samplesheet/test_samplesheet.csv + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results From 637570a589ca6222f6cfc5cea1df1f626ad58613 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Thu, 11 Apr 2024 14:47:14 +0800 Subject: [PATCH 33/40] added -stub back to the nextflow run command --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 48fe5d0..08622fd 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -69,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results From e609cc43cf268a2da7996f7cb8d63633d3e283a8 Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Thu, 11 Apr 2024 14:56:32 +0800 Subject: [PATCH 34/40] added echo to print pipeline download command --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 08622fd..2009063 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -69,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: echo nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results From 9a24dd1597d6188ff7ecc4b2835a1b56d4f4732d Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 12 Apr 2024 06:56:10 +0800 Subject: [PATCH 35/40] removed the echo from the pipeline download command --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2009063..08622fd 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -69,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: echo nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results From cd0b46c50714170199ba487b1ca9be3e0e09de9b Mon Sep 17 00:00:00 2001 From: Adam Bennett Date: Fri, 12 Apr 2024 09:30:31 +0800 Subject: [PATCH 36/40] added pattern to ncbidownload_group's input validation to allow a comma separated list of groups --- nextflow_schema.json | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 03f9fa8..b49f205 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -372,19 +372,7 @@ "type": "string", "default": "all", "description": "The NCBI taxonomic groups to download. Options include 'all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', and 'viral'. A comma-separated list is also valid (e.g., 'bacteria,viral').", - "enum": [ - "all", - "archaea", - "bacteria", - "fungi", - "invertebrate", - "metagenomes", - "plant", - "protozoa", - "vertebrate_mammalian", - "vertebrate_other", - "viral" - ] + "pattern": "^(?:[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+(?:,[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+)*)?$" }, "ncbidownload_section": { "type": "string", From 288be93223eb02a77249821ffff9d79b2e18bf7d Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Mon, 15 Apr 2024 13:46:57 +0800 Subject: [PATCH 37/40] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index b49f205..2db9bd0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -372,7 +372,7 @@ "type": "string", "default": "all", "description": "The NCBI taxonomic groups to download. Options include 'all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', and 'viral'. A comma-separated list is also valid (e.g., 'bacteria,viral').", - "pattern": "^(?:[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+(?:,[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+)*)?$" + "pattern": "^((all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral)?,?)*(? Date: Fri, 26 Apr 2024 12:23:40 +0800 Subject: [PATCH 38/40] Changes based on PR #41 reviews --- .github/workflows/release-announcements.yml | 2 +- CHANGELOG.md | 3 ++- main.nf | 1 - 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index d468aea..788d134 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/CHANGELOG.md b/CHANGELOG.md index 2cb4f5e..82dc84c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,13 +3,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 1.0.1 - 2024-03-22 +## 1.0.1 - 2024-03-23 Minor release after nf-core template 2.13.1 update ### `Added` - [#36] - Merged nf-core template 2.13.1 update +- [#36] - Multiqc version changed 1.19 -> 1.21 ### `Fixed` diff --git a/main.nf b/main.nf index 40f3aca..7c5dfb5 100644 --- a/main.nf +++ b/main.nf @@ -29,7 +29,6 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_read ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// TODO nf-core: Remove this line if you don't need a FASTA file // This is an example of how to use getGenomeAttribute() to fetch parameters // from igenomes.config using `--genome` if (!params.fasta) { From a50755811a9d773e5effa974b6c3bf25a0600622 Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Sat, 27 Apr 2024 07:22:14 +0800 Subject: [PATCH 39/40] Update CHANGELOG.md Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 82dc84c..838898e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 1.0.1 - 2024-03-23 +## 1.0.1 - 2024-03-26 Minor release after nf-core template 2.13.1 update From e55115b94ffb4ccf222bb14870c6e597ebf66126 Mon Sep 17 00:00:00 2001 From: Adam Bennett <43841526+a4000@users.noreply.github.com> Date: Sat, 27 Apr 2024 07:23:07 +0800 Subject: [PATCH 40/40] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 838898e..4b80ccf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 1.0.1 - 2024-03-26 +## 1.0.1 - 2024-04-26 Minor release after nf-core template 2.13.1 update
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