2.0.0 Release #13

emarinier · 2024-02-14T20:20:50Z

No description provided.

Updating the Documentation

Small Changes for Release

2.0.0 Release

github-actions · 2024-02-14T20:24:03Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ac17cb

+| ✅ 134 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.0.0
schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/snvphylnfc/master/nextflow_schema.json
Found https://raw.githubusercontent.com/phac-nml/snvphylnfc/main/nextflow_schema.json

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-snvphylnfc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-snvphylnfc_logo_light.png
files_exist - File is ignored: docs/images/nf-core-snvphylnfc_logo_dark.png
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-snvphylnfc_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-snvphylnfc_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-snvphylnfc_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/snvphylnfc/snvphylnfc/.github/workflows/awstest.yml
actions_awsfulltest - actions_awsfulltest
pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: lib/WorkflowSnvphylnfc.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-snvphylnfc_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.min_coverage_depth= 15
nextflow_config - Config default value correct: params.min_mapping_percent_cov= 80
nextflow_config - Config default value correct: params.min_mean_mapping_quality= 30
nextflow_config - Config default value correct: params.window_size= 500
nextflow_config - Config default value correct: params.density_threshold= 2
nextflow_config - Config default value correct: params.snv_abundance_ratio= 0.75
nextflow_config - Config default value correct: params.min_repeat_length= 150
nextflow_config - Config default value correct: params.min_repeat_pid= 90
nextflow_config - Config default value correct: params.max_cpus= 4
nextflow_config - Config default value correct: params.max_memory= 2.GB
nextflow_config - Config default value correct: params.max_time= 1.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
template_strings - Did not find any Jinja template strings (111 files)
schema_lint - Schema lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.12.1
Run at 2024-02-14 20:23:45

emarinier added 30 commits December 11, 2023 11:24

Indexing and finding repeats.

04092ef

smalt

4568136

sorting BAMs

ca3595f

freebayes

b96cb03

freebayes post processing

ee18a09

bcftools, freebayes, mpileup

dce1714

added remaining modules

15c08a4

Changing example data.

9c6266e

Switching bash-only modules from phoenix container to python.

906cc61

Adding legal requirements for including Apache v2 work.

9a2b956

Attempting to correctly attribute this Python file.

1ec25ca

Attributing the main workflow.

14ce635

Trying to support single end reads.

43c1f90

Single end, minimum coverage 5x.

4dafaa8

Switching from Phoenix container to Python.

e0fdae9

Formatting, schema, linting.

b0b9df9

Formatting

39d597f

Linting

700811f

Trying to avoid EditorConfig check the LICENSE file.

2f0cdbe

Trying to avoid EditorConfig check the LICENSE file.

e4ac2ad

docker->singularity for testing

9beb648

phyml docker debugging

b0e96ab

Removing commented-out singularity container for PhyML.

9ed0801

Changing PhyML to 3.3.20211231--hee9e358_1 docker container.

c128b5b

Trigger CI

583f76f

Linting

94e6104

Adding variable CPUs.

dc40936

Fixing variable CPUs.

f9490ad

Adding coverage, quality mapping, and VCF abundance pipeline parameters.

ffc0dac

Adding pipeline parameters for the find repeats module.

386cd01

emarinier and others added 26 commits February 8, 2024 12:58

Fixing samplesheet example.

defa1fb

prettier

2ee76c1

Updating citations.

9aec099

Mandatory reference.

19be152

removing 'and be included in the analysis'.

f634f02

adding 'on the reference genome'.

2be4bd2

test profile, profile and revision parameters

a114e65

main.nf to phac-nml/snvphylnfc

f9d87fc

irida to iridanext

d47cead

main.nf to phac-nml/snvphylnfc

887e53d

prettier

be65dc6

Merge pull request #10 from phac-nml/docs

850cbbc

Updating the Documentation

Updating samplesheet.

db66e67

assembly -> reference_assembly

7feedd3

vcf2snv single->high

ae1b283

Compressed VCFs

7b24e77

Removing old module for compressing mpileup files.

b920e34

prettier

8a15044

Removing import

637fd86

Merge pull request #11 from phac-nml/release-changes

6df411a

Small Changes for Release

Updating default parameters.

611667a

Version numbers.

bfb8116

Updating links to data.

0603d0c

Version 2.0.0

0353b9e

Changelog, pipeline description.

cb4a47f

Merge pull request #12 from phac-nml/release

675560e

2.0.0 Release

emarinier self-assigned this Feb 14, 2024

Merge branch 'main' into dev

0ac17cb

emarinier merged commit 55c5cb3 into main Feb 14, 2024
9 checks passed

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2.0.0 Release #13

2.0.0 Release #13

emarinier commented Feb 14, 2024

github-actions bot commented Feb 14, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

2.0.0 Release #13

2.0.0 Release #13

Conversation

emarinier commented Feb 14, 2024

github-actions bot commented Feb 14, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented Feb 14, 2024 •

edited

Loading

`nf-core lint` overall result: Passed ✅ ⚠️