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Make replicates explicit in samplesheet #349

Merged
merged 12 commits into from
Jun 22, 2023
Merged

Make replicates explicit in samplesheet #349

merged 12 commits into from
Jun 22, 2023

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JoseEspinosa
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@JoseEspinosa JoseEspinosa commented Jun 20, 2023 •
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Make replicates explicit and add control_replicate field to samplesheet.
Closes #343

PR checklist

  • This comment contains a description of changes (with reason).
  • 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.

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github-actions bot commented Jun 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2715175

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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 passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-22 12:03:21

@JoseEspinosa JoseEspinosa marked this pull request as ready for review June 21, 2023 13:48
bjlang
bjlang approved these changes Jun 22, 2023
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conf/test_full.config
@@ -17,7 +17,7 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.0/samplesheet_full.csv'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.1/samplesheet_full.csv'
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This file isn't in the correct format:
EZH2_IP_NTKO,s3://ngi-igenomes/test-data/chipseq/SRX541384_T1.fastq.gz,,1,EZH2,INPUT_NTKO_REP1

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Good spot, corrected now, thanks!

@JoseEspinosa JoseEspinosa merged commit 0cf949c into nf-core:dev Jun 22, 2023
@JoseEspinosa JoseEspinosa deleted the explicit_rep branch June 22, 2023 14:29
@JoseEspinosa JoseEspinosa mentioned this pull request Jul 13, 2023
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@bjlang bjlang bjlang approved these changes

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@JoseEspinosa @bjlang