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Update concat_vcf/main.nf #457

Merged
merged 1 commit into from
Nov 24, 2021
Merged

Update concat_vcf/main.nf #457

merged 1 commit into from
Nov 24, 2021

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nickhsmith
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A fix in response to #456

htslib is a dependency of bcftools, so all of the functionality should be maintained. The script concatenateVCFs.sh uses bcftools, so it must be included in the conda env or singularity/docker image.

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github-actions bot commented Nov 24, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 35f121b

+| ✅ 135 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • 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 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 main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable
  • pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in main.nf: List additional required output channels/values here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-24 12:35:50

@maxulysse maxulysse merged commit 6890014 into nf-core:dev Nov 24, 2021
@nickhsmith nickhsmith deleted the concat_vcf_tool_update branch November 24, 2021 14:21
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@maxulysse maxulysse maxulysse approved these changes

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@nickhsmith @maxulysse