From eb301b41c17a21ee7961a0c85d6774bd0d449182 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 31 Jan 2025 12:09:40 +0100 Subject: [PATCH] removing flagstat again (without messy dev merge) --- workflows/eager.nf | 8 -------- 1 file changed, 8 deletions(-) diff --git a/workflows/eager.nf b/workflows/eager.nf index 6ff32b5e..0651e5ce 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -57,7 +57,6 @@ include { FALCO } from '../modules include { MTNUCRATIO } from '../modules/nf-core/mtnucratio/main' include { HOST_REMOVAL } from '../modules/local/host_removal' include { ENDORSPY } from '../modules/nf-core/endorspy/main' -include { SAMTOOLS_FLAGSTAT as SAMTOOLS_FLAGSTATS_BAM_INPUT } from '../modules/nf-core/samtools/flagstat/main' include { BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_DEPTH } from '../modules/nf-core/bedtools/coverage/main' include { BEDTOOLS_COVERAGE as BEDTOOLS_COVERAGE_BREADTH } from '../modules/nf-core/bedtools/coverage/main' include { SAMTOOLS_VIEW_GENOME } from '../modules/local/samtools_view_genome.nf' @@ -203,13 +202,6 @@ workflow EAGER { ch_bams_from_input = ch_samplesheet_bams.join(SAMTOOLS_INDEX_BAM_INPUT.out.bai) } - // - // MODULE: flagstats of user supplied input BAMs - // Maybe remove if subworkflow is already running it? - // SAMTOOLS_FLAGSTATS_BAM_INPUT ( ch_bams_from_input ) - // ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTATS_BAM_INPUT.out.versions ) - // ch_flagstat_input_bam = SAMTOOLS_FLAGSTATS_BAM_INPUT.out.flagstat // For endorspy - // SUBWORKFLOW: Merging lanes for ch_bams_from_input MERGE_LANES_INPUTBAM(ch_bams_from_input)