From 7fd821c41c0d1e8539a907db1090b5b96d7dd2ac Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 7 Feb 2025 11:32:07 +0100 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Thiseas C. Lamnidis --- subworkflows/local/merge_lanes_inputbam.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/merge_lanes_inputbam.nf b/subworkflows/local/merge_lanes_inputbam.nf index 58be90c5..cccef0e1 100644 --- a/subworkflows/local/merge_lanes_inputbam.nf +++ b/subworkflows/local/merge_lanes_inputbam.nf @@ -2,10 +2,10 @@ // Prepare reference indexing for downstream // -include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_LANES } from '../../modules/nf-core/samtools/merge/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_MERGED_LANES } from '../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MERGED_LANES } from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT_MAPPED } from '../../modules/nf-core/samtools/flagstat/main' +include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_LANES } from '../../modules/nf-core/samtools/merge/main' +include { SAMTOOLS_SORT as SAMTOOLS_SORT_MERGED_LANES } from '../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MERGED_LANES } from '../../modules/nf-core/samtools/index/main' +include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTAT_MAPPED } from '../../modules/nf-core/samtools/flagstat/main' workflow MERGE_LANES_INPUTBAM { take: @@ -50,7 +50,7 @@ workflow MERGE_LANES_INPUTBAM { emit: bam = ch_mapped_bam // [ [ meta ], bam ] - bai = ch_mapped_bai // [ [ meta ], bai ] + bai = ch_mapped_bai // [ [ meta ], bai/csi ] flagstat = SAMTOOLS_FLAGSTAT_MAPPED.out.flagstat // [ [ meta ], stats ] mqc = ch_multiqc_files versions = ch_versions