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Add new parameters --reference and --protospacer #45

Merged
merged 6 commits into from
Jun 28, 2023
Merged

Add new parameters --reference and --protospacer #45

merged 6 commits into from
Jun 28, 2023

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mirpedrol
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Add new parameters --reference and --protospacer.
Close #43

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/crisprseq 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).

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github-actions bot commented Jun 27, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ea4319a

+| ✅ 154 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-06-27 13:05:14

@mirpedrol
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@nf-core-bot fix linting please!

LaurenceKuhl
LaurenceKuhl reviewed Jun 27, 2023
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workflows/crisprseq_targeted.nf
.join(INPUT_CHECK.out.protospacer
.map {
meta, fastq ->
[ meta - meta.subMap('id') + [id: meta.id.split('_')[0..-2].join('_')], fastq ]
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I'm not sure what line 150 does?

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When reading the input sample sheet, we add a _T<number> suffix to the sample name (see https://github.com/nf-core/crisprseq/blob/master/bin/check_samplesheet.py#L120). We use this to concatenate the fastq files if one sample has more than fastq file. Here we are removing this suffix so that the meta map in other channels matches the one of reads.

@mirpedrol mirpedrol merged commit 46760d5 into nf-core:dev Jun 28, 2023
@mirpedrol mirpedrol deleted the reference-param branch June 28, 2023 11:06
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@LaurenceKuhl LaurenceKuhl LaurenceKuhl approved these changes

@msanvicente msanvicente Awaiting requested review from msanvicente

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@mirpedrol @LaurenceKuhl @nf-core-bot