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Added option to add a custom annotation, clarified multiQC results and fixed issues #401

Merged
merged 31 commits into from
Apr 22, 2024
Merged

Added option to add a custom annotation, clarified multiQC results and fixed issues #401

merged 31 commits into from
Apr 22, 2024

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svarona
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@svarona svarona commented Oct 23, 2023 •
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Included issue #390, issue #336 enhancements and issue #419

  • Added new param to add a custom annotation (gtf or gff format)
  • Added new subworkflow to perform the additional annotation
  • Allowed SNPEFF_BUILD process to detect wether annotation is in gtf or gff format
  • Fixed variants_long_table so it won't select first annotation feature only, but remove the features that are not upstream or downstream
  • Added a clearly description of variants_long_table formats and content for both nanopore and illumina.
  • Clarify #SNPs and #INDELS in the illumina's multiqc

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
  • 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).

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github-actions bot commented Oct 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9cacdc2

+| ✅ 176 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 247]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-22 13:26:43

@svarona svarona marked this pull request as ready for review January 18, 2024 16:57
@svarona svarona changed the title Added option to add a custom annotation Added option to add a custom annotation and clarified multiQC results Feb 16, 2024
maxulysse
maxulysse reviewed Apr 2, 2024
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.github/workflows/ci.yml Outdated
Comment on lines 87 to 90
- name: Download GTF for additional annotation
run: |
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz

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If I'm not misunderstanding, you're downloading this every time in this matrix.
Can you add an if statement on the params for this step?

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Sure! I also added it in nanopore when it downloads the medaka model. Thanks for the suggestion!

maxulysse
maxulysse reviewed Apr 2, 2024
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Superb work, I'm not a super fan of the name for this new params: --additional_annot
Why not --additional_annotation, it's not that much longer.

maxulysse
maxulysse reviewed Apr 2, 2024
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nextflow_schema.json
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+(\\.gff|\\.gtf)(\\.gz)?$",
"description": "Full path to additional annotation file in GTF or GFF format.",
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You could mention the optional .gz.
I assume there's no need to decompress in such case?

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It is the same format as the --gff param

Should I add the .gz in the description for both? Both of them have a GUNZIP_GFF process in the case they are compressed.

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svarona commented Apr 22, 2024

Superb work, I'm not a super fan of the name for this new params: --additional_annot Why not --additional_annotation, it's not that much longer.

Done! ✔️

@svarona svarona changed the title Added option to add a custom annotation and clarified multiQC results Added option to add a custom annotation, clarified multiQC results and fixed issues Apr 22, 2024
@svarona svarona mentioned this pull request Apr 22, 2024
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@svarona svarona merged commit 6dee7cb into nf-core:dev Apr 22, 2024
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@svarona svarona deleted the custom_gtf branch April 22, 2024 14:00
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