Merge pull request #186 from nf-core/dev

1.1.1 - LATÜRNICH

.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.

.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/pangenome then the best place to ask is on the nf-core Slack [#pangenome](https://nfcore.slack.com/channels/pangenome) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/pangenome then the best place to ask is on the nf-core Slack [#pangenome](https://nfcore.slack.com/channels/pangenome) 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 <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
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pang
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pangenome/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/pangenome _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 <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 <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.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
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -28,7 +28,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |

.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: |

.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 }}"
 
@@ -50,7 +50,7 @@ jobs:
     strategy:
       matrix:
         parameters:
-          - '--vcf_spec "gi|568815561:#,gi|568815567:#"'
+          - '--vcf_spec "gi|568815561:5,gi|568815567:25"'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -164,7 +164,7 @@ jobs:
         parameters:
           - "--communities"
           - "--communities --wfmash_chunks 2"
-          - '--communities --vcf_spec "gi|568815561:#,gi|568815567:#"'
+          - '--communities --vcf_spec "gi|568815561:5,gi|568815567:25"'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3

.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@v2
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:

.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:

.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:

.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

CHANGELOG.md

@@ -2,6 +2,16 @@
 
 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).
 
+## 1.1.1 - LATÜRNICH
+
+This release fixes some important bugs:
+
+- Per default, we set the number of mappings in `wfmash` to `1`. Previously, this was set to the given number of haplotypes.
+- To complement the issue above, there is a new parameter `wfmash_n_mappings` with default `1`.
+- `bcftools` in the `VG_DECONSTRUCT` module was updated to the most recent version `1.19` to prevent errors like `corrupted size vs. prev_size`.
+- Fixed some problems with the delimiter in `VG_DECONSTRUCT` so that the parameters given by `--vcf-spec` are now applied correctly.
+- Updated to nf-core template version 2.13.1
+
 ## 1.1.0 - Schmuddlweddr
 
 This release mostly contains updates of the respective modules. Functional updates are the following:

README.md

@@ -7,12 +7,12 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/pangenome/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pangenome/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/pangenome/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pangenome/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/pangenome/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.8202636-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.8202636)
-
+[![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/pangenome)
+[![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/pangenome)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pangenome-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pangenome)[![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)
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pangenome/releases/tag/1.1.0" target="_blank">nf-core/pangenome</a>
+  This report has been generated by the <a href="https://github.com/nf-core/pangenome/releases/tag/1.1.1" target="_blank">nf-core/pangenome</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/pangenome/1.1.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/pangenome/1.1.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pangenome-methods-description":
     order: -1000

conf/hla.config

@@ -15,7 +15,7 @@ process {
     }
 
     withName:'SMOOTHXG' {
-        cpus = 4
+        cpus = 8
         memory = 8.GB
 //        container = "ghcr.io/pangenome/pggb:20230331171956507fc0"
     }

conf/modules.config

@@ -102,7 +102,7 @@ process {
     withName: WFMASH_MAP_ALIGN {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -114,6 +114,7 @@ process {
                 "${wfmash_sparse_map_cmd}",
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -126,7 +127,7 @@ process {
     withName: WFMASH_MAP {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -139,6 +140,7 @@ process {
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-m",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -151,7 +153,7 @@ process {
     withName: WFMASH_MAP_COMMUNITY {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -164,6 +166,7 @@ process {
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "-m",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [
@@ -185,7 +188,7 @@ process {
     withName: WFMASH_ALIGN {
         ext.args = {
             [
-                "-n ${params.n_haplotypes - 1}",
+                "-n ${params.wfmash_n_mappings}",
                 "-s ${parse_int(params.wfmash_segment_length)}",
                 "-p ${params.wfmash_map_pct_id}",
                 params.wfmash_merge_segments   ? "-M"                                : "",
@@ -198,6 +201,7 @@ process {
                 params.wfmash_temp_dir         ? "-B ${wfmash_temp_dir}"             : "",
                 "--invert-filtering",
                 "-2 ${params.wfmash_hg_filter_ani_diff}",
+                "--lower-triangular",
             ].join(" ").trim()
         }
         publishDir = [

modules.json

@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290",
+                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     },
                     "odgi/build": {
@@ -91,17 +91,17 @@
                 "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"]
                     }
                 }

modules/local/vg_deconstruct/main.nf

@@ -29,7 +29,7 @@ process VG_DECONSTRUCT {
         'https://depot.galaxyproject.org/singularity/pggb:0.5.3--hdfd78af_2':
         'quay.io/biocontainers/pggb:0.5.3--hdfd78af_2' }"
 */
-    container "ghcr.io/pangenome/pggb:20230819064109936a2c"
+    container "ghcr.io/pangenome/pggb:20240313103308d2dc38"
 
     input:
     tuple val(meta), path(graph), val(vcf_spec)
@@ -47,16 +47,20 @@ process VG_DECONSTRUCT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     ref=\$(echo "$vcf_spec" | cut -f 1 -d:)
-    delim=\$(echo "$vcf_spec" | cut -f 2 -d:)
-    pop_length=\$(echo "$vcf_spec" | cut -f 3 -d:)
+    if [[ "$vcf_spec" == *":"* ]]; then
+        pop_length=\$(echo "$vcf_spec" | cut -f 2 -d:)
+    else
+        pop_length=""
+    fi
 
     if [[ -z \$pop_length ]]; then
         pop_length=0
     fi
 
     vcf="${graph}".\$(echo \$ref | tr '/|' '_').vcf
-    vg deconstruct -P \$ref -H \$delim -e -a -t "${task.cpus}" "${graph}" > \$vcf
+    vg deconstruct -P \$ref -H "#" -e -a -t "${task.cpus}" "${graph}" > \$vcf
     bcftools stats \$vcf > \$vcf.stats
+
     if [[ \$pop_length -gt 0 ]]; then
         vcf_decomposed=${graph}.final.\$(echo \$ref | tr '/|' '_').decomposed.vcf
         vcf_decomposed_tmp=\$vcf_decomposed.tmp.vcf
@@ -65,7 +69,7 @@ process VG_DECONSTRUCT {
         #TODO: to remove when vcfwave will be bug-free
         # The TYPE info sometimes is wrong/missing
         # There are variants without the ALT allele
-        bcftools sort \$vcf_decomposed_tmp | bcftools annotate -x INFO/TYPE \$vcf_decomposed_tmp  | awk '\$5 != "."' > \$vcf_decomposed
+        bcftools sort \$vcf_decomposed_tmp | bcftools annotate -x INFO/TYPE | awk '\$5 != "."' > \$vcf_decomposed
         rm \$vcf_decomposed_tmp \$vcf.gz
         bcftools stats \$vcf_decomposed > \$vcf_decomposed.stats
     fi