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Fix index lacking a meta map causing igenomes and premade indexes to fail #109

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merged 6 commits into from Feb 17, 2023
Merged

Fix index lacking a meta map causing igenomes and premade indexes to fail #109

merged 6 commits into from Feb 17, 2023

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edmundmiller
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Closes #106

@edmundmiller edmundmiller self-assigned this Feb 17, 2023
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github-actions bot commented Feb 17, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0fdd39b

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.1.1'
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • 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 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: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-02-17 02:07:27

@edmundmiller edmundmiller linked an issue Feb 17, 2023 that may be closed by this pull request
Error executing process > 'NFCORE_NASCENT:NASCENT:ALIGN_BWA:BWA_MEM (1)' #106
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FriederikeHanssen
FriederikeHanssen reviewed Feb 17, 2023
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subworkflows/local/prepare_genome.nf
@@ -106,7 +108,8 @@ workflow PREPARE_GENOME {
ch_bwa_index = UNTAR_BWA_INDEX ( [ [:], params.bwamem2_index ] ).untar
ch_versions = ch_versions.mix(UNTAR_BWA_INDEX.out.versions)
} else {
ch_bwa_index = file(params.bwamem2_index)
// TODO Give the meta from basename or genome?
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This is future-Edmunds problem? :D

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Yeah, I'm not sure how it's supposed to be handled and what the point of adding a meta map to the indexes was except to bring pain. 😩

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I think it was all the metagenomics people's fault, that want to use multiple fastas or whatever. Insanity!

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we just used the file name as stand-in basically https://github.com/nf-core/sarek/blob/c87f4eb694a7183e4f99c70fca0f1d4e91750b33/subworkflows/local/prepare_genome/main.nf#L48

FriederikeHanssen
FriederikeHanssen approved these changes Feb 17, 2023
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looks good

@edmundmiller edmundmiller changed the title Fix/bwa index Fix index lacking a meta map causing igenomes and premade indexes to fail Feb 17, 2023
@edmundmiller edmundmiller merged commit d8e2684 into dev Feb 17, 2023
@edmundmiller edmundmiller deleted the fix/bwa_index branch February 17, 2023 14:48
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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Error executing process > 'NFCORE_NASCENT:NASCENT:ALIGN_BWA:BWA_MEM (1)'
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@edmundmiller @FriederikeHanssen