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Fastq-subsample-index-fix #1006

Merged
merged 1 commit into from
Apr 24, 2023
Merged

Fastq-subsample-index-fix #1006

merged 1 commit into from
Apr 24, 2023

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robsyme
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@robsyme robsyme commented Apr 22, 2023

Without this fix, we risk indexing the genome for each sample rather than just once for all samples.

Fixex #1003

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/rnaseq 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).

@robsyme
Ensure that FASTQ_SUBSAMPLE_FQ_SALMON is provided a value channel for
92dde77 
genome fastq.

Without this fix, we risk indexing the genome for each sample rather
than just once for all samples.
@robsyme robsyme changed the base branch from master to dev April 22, 2023 21:55
@nf-core nf-core deleted a comment from github-actions bot Apr 22, 2023
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github-actions bot commented Apr 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 92dde77

+| ✅ 147 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-22 21:57:13

@robsyme robsyme mentioned this pull request Apr 22, 2023
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drpatelh
drpatelh approved these changes Apr 24, 2023
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Thanks @robsyme ! 🚀

@drpatelh drpatelh marked this pull request as ready for review April 24, 2023 08:58
@drpatelh drpatelh merged commit 9327ddc into dev Apr 24, 2023
@drpatelh drpatelh deleted the fastq-subsample-index-fix branch November 21, 2023 09:46
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