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build: nf-core modules update samtools/sort #147

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build: nf-core modules update samtools/sort #147

wants to merge 1 commit into from

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edmundmiller
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@edmundmiller edmundmiller commented Jul 29, 2024 •
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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).

Running this pipeline for someone else, and I'm getting

samtools sort: couldn't allocate memory for bam_mem

I'll link the module update PR that fixed this.

@edmundmiller edmundmiller self-assigned this Jul 29, 2024
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github-actions bot commented Jul 29, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 7ab7b7c

+| ✅ 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: 1.0.3
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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.
  • nfcore_yml - nf-core version not set in .nf-core.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-29 22:14:51

@edmundmiller
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Seems to still be broken on my end 🤷🏻‍♂️

@jma1991
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jma1991 commented Aug 21, 2024

Closed in favour of #149

@jma1991 jma1991 closed this Aug 21, 2024
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@edmundmiller @jma1991