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Clean up config file #307

Merged
merged 6 commits into from
Jan 26, 2024
Merged

Clean up config file #307

merged 6 commits into from
Jan 26, 2024

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grst
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@grst grst commented Jan 26, 2024 •
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Reorganize the config

  • it was in completely random order making it hard to follow along the workflow
  • some directives were duplicated
  • the if-branching is not required anymore since in the latest nf-core template the missing process warnings are hidden.
  • the folder structure was confusing, I couldn't really say what was generated by which part of the pipeline

New output structure

results
├── bowtie_index
│   ├── genome
│   ├── mirna_hairpin
│   └── mirna_mature
├── fastp
├── fastqc
│   ├── raw
│   └── trimmed
├── genome_quant
│   └── bam
├── mirna_quant
│   ├── bam
│   ├── edger_qc
│   ├── mirtop
│   ├── reference
│   └── seqcluster
├── mirtrace
│   ├── qc_passed_reads.all.collapsed
│   └── qc_passed_reads.rnatype_unknown.collapsed
├── multiqc
│   ├── multiqc_data
│   └── multiqc_plots
├── pipeline_info
└── umi_dedup
    ├── bam_deduplicated
    ├── bam_mapped
    ├── bam_mapped_sorted
    ├── fastq_deduplicated
    └── fastq_extracted_umi

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/smrnaseq 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>).
  • 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).

grst added 3 commits January 26, 2024 10:38
@grst
Remove redundant fastq option
4b2bf89
@grst
Clean up config
17f2ae5 
Replicating the if/else logic from the main workflow is
not necessary, since now, by default
nextflow.enable.configProcessNamesValidation = false
@grst
WIP reorganize config
306cd4e
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github-actions bot commented Jan 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ec22f39

+| ✅ 162 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.3.0
  • pipeline_todos - TODO string in WorkflowSmrnaseq.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: save_merged

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-26 14:49:15

@grst grst changed the title Grst fixes Clean up config file Jan 26, 2024
@grst grst marked this pull request as ready for review January 26, 2024 13:50
@grst grst mentioned this pull request Jan 26, 2024
Merged
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@apeltzer apeltzer merged commit 6d85ddf into dev Jan 26, 2024
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@apeltzer apeltzer deleted the grst-fixes branch January 26, 2024 15:14
@apeltzer apeltzer mentioned this pull request Jan 30, 2024
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@apeltzer apeltzer apeltzer approved these changes

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