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Published 20 hours ago • verified publisher icon nf-core

don't throw error about csi indexing needed when csi indexing has been specified

Open adf-ncgr opened this issue 2 years ago • 1 comments

PR checklist

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

digging into #855 more on our side, we found that the .nextflow.log contained the error:

Aug-08 22:52:30.870 [Actor Thread 110] ERROR nextflow.Nextflow - ============================================================================= Contig longer than 512000000bp found in reference genome!

pissa.Cameor.gnm1.chr5LG3: 579269071

Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.

Please see: https://github.com/nf-core/rnaseq/issues/744

BUT, this was despite our having specified --bam_csi_index in the pipeline invocation. Making the little tweak in this PR seems to have made the pipeline run to completion using --bam_csi_index

adf-ncgr avatar Aug 09 '22 17:08 adf-ncgr

I'm also getting this error with v3.8.1 even though I've specified --bam_csi_index as one of the parameters

brettChapman avatar Aug 15 '22 02:08 brettChapman

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 1093260

+| ✅ 145 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

:grey_question: Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-08-17 11:18:58

github-actions[bot] avatar Aug 17 '22 11:08 github-actions[bot]