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Update samtools module #149

Merged
merged 7 commits into from
Aug 21, 2024
Merged

Update samtools module #149

merged 7 commits into from
Aug 21, 2024

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jma1991
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@jma1991 jma1991 commented Aug 21, 2024

This pull request addresses issue #145 and potentially issue #144

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/rnasplice branch on the 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>).
  • 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.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Aug 21, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 698152d

+| ✅ 237 tests passed       |+
!| ❗   5 tests had warnings |!
-| ❌  21 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/WorkflowRnasplice.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.igenomes_base is set as s3://ngi-igenomes/igenomes in nextflow_schema.json but is s3://ngi-igenomes/igenomes/ in nextflow.config.
  • nextflow_config - Config default value incorrect: params.aligner is set as star in nextflow_schema.json but is star_salmon in nextflow.config.
  • nextflow_config - Config default value incorrect: params.min_samps_gene_expr is set as 6 in nextflow_schema.json but is 4 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.min_samps_feature_expr is set as 0 in nextflow_schema.json but is 2 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.min_samps_feature_prop is set as 0 in nextflow_schema.json but is 2 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.miso_genes is set as ENSG00000004961, ENSG00000005302 in nextflow_schema.json but is ENSG00000004961, ENSG00000005302, ENSG00000147403 in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-rnasplice_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnasplice_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-rnasplice_logo_dark.png does not match the template
  • modules_config - conf/modules.config contains withName:CAT_ADDITIONAL_FASTA, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.4
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowRnasplice.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • nfcore_yml - nf-core version not set in .nf-core.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-21 19:07:07

@jma1991 jma1991 merged commit 05a0402 into nf-core:dev Aug 21, 2024
21 of 22 checks passed
@jma1991 jma1991 deleted the update-samtools-module branch August 21, 2024 19:27
@jma1991 jma1991 mentioned this pull request Aug 21, 2024
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