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Quick Version Release 1.0.4 - Pipeline issue arose in 1.0.3 where only one sample was processed #58

Merged
merged 3 commits into from
Jun 26, 2023
Merged

Quick Version Release 1.0.4 - Pipeline issue arose in 1.0.3 where only one sample was processed #58

merged 3 commits into from
Jun 26, 2023

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DSchreyer
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Version Release 1.0.4

v1.0.4 - [2023-06-26]

Added

Fixed

  • Bug that the pipeline only runs with one sample when Picard Markduplicates is used

Dependencies

Deprecated

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/circdna branch on the nf-core/test-datasets repository.
  • [ x] 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 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 621bef1

+| ✅ 157 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.4'
  • 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_exist - File is ignored: assets/multiqc_config.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-26 11:20:24

maxulysse
maxulysse reviewed Jun 26, 2023
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workflows/circdna.nf
@@ -23,7 +23,7 @@ if (!(params.input_format == "FASTQ" | params.input_format == "BAM")) {
}

// Modify fasta channel to include meta data
ch_fasta_meta = ch_fasta.map{ it -> [[id:it[0].baseName], it] }
ch_fasta_meta = ch_fasta.map{ it -> [[id:it[0].baseName], it] }.collect()
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good catch

sguizard
sguizard approved these changes Jun 26, 2023
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LGTM

@DSchreyer DSchreyer merged commit 09a5015 into master Jun 26, 2023
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@maxulysse maxulysse maxulysse approved these changes

@sguizard sguizard sguizard approved these changes

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3 participants
@DSchreyer @maxulysse @sguizard