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Extract reads for viral taxids #15

Merged
merged 54 commits into from
Jun 5, 2024
Merged

Extract reads for viral taxids #15

merged 54 commits into from
Jun 5, 2024

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LilyAnderssonLee
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@LilyAnderssonLee LilyAnderssonLee commented Apr 3, 2024 •
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This PR solved these issues:

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/metaval branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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 Apr 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f095068

+| ✅ 158 tests passed       |+
#| ❔ 177 tests were ignored |#
!| ❗  23 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • 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
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
  • schema_description - Ungrouped param in schema: extract_kraken2_reads
  • schema_description - Ungrouped param in schema: extract_centrifuge_reads
  • schema_description - Ungrouped param in schema: extract_diamond_reads
  • schema_description - Ungrouped param in schema: fastq_output

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-05 11:08:48

@LilyAnderssonLee LilyAnderssonLee mentioned this pull request May 6, 2024
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@LilyAnderssonLee LilyAnderssonLee changed the title Add modules to extract reads Extract reads for viral taxids May 6, 2024
@LilyAnderssonLee LilyAnderssonLee requested a review from lokeshbio May 6, 2024 13:42
@LilyAnderssonLee LilyAnderssonLee requested a review from sofstam May 6, 2024 13:53
maxulysse
maxulysse reviewed May 6, 2024
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maxulysse
maxulysse reviewed May 6, 2024
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sofstam
sofstam reviewed May 6, 2024
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Nice job!

I made a few suggestions and added some comments/questions.

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LilyAnderssonLee and others added 2 commits May 7, 2024 08:48
@LilyAnderssonLee @maxulysse
Update nextflow.config
e52b3bb 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@LilyAnderssonLee @sofstam
Update README.md
aa03a5c 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
sofstam
sofstam reviewed Jun 3, 2024
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Few more comments/suggestions

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LilyAnderssonLee and others added 8 commits June 3, 2024 14:04
@LilyAnderssonLee @sofstam
Update docs/usage.md
38da4b4 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update nextflow_schema.json
d2f7024 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update docs/usage.md
8a4865e 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update README.md
af4cbc4 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update modules/local/extract_viral_taxid.nf
3ab0681 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update docs/usage.md
4aba487 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee
update document
ed1fc7b
@LilyAnderssonLee
update README
1ea35aa
sofstam
sofstam approved these changes Jun 5, 2024
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🌟

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LilyAnderssonLee and others added 4 commits June 5, 2024 13:06
@LilyAnderssonLee @sofstam
Update CHANGELOG.md
a6137ea 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update CHANGELOG.md
c5bc866 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update CHANGELOG.md
b202ef8 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee @sofstam
Update CHANGELOG.md
f095068 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@LilyAnderssonLee LilyAnderssonLee merged commit 68c89c9 into dev Jun 5, 2024
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This was referenced Jun 5, 2024
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@LilyAnderssonLee LilyAnderssonLee deleted the krakentools branch October 15, 2024 13:11
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@maxulysse maxulysse maxulysse left review comments

@sofstam sofstam sofstam approved these changes

@lokeshbio lokeshbio lokeshbio approved these changes

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@LilyAnderssonLee @maxulysse @lokeshbio @sofstam