From 76f01afb9146b9b2d65051503094023b9c298911 Mon Sep 17 00:00:00 2001 From: Judith Ballesteros Date: Fri, 7 Feb 2025 10:47:54 +0100 Subject: [PATCH] setting empty channel for flagstats --- workflows/eager.nf | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/workflows/eager.nf b/workflows/eager.nf index 54e12d26..34601233 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -207,10 +207,11 @@ workflow EAGER { MERGE_LANES_INPUTBAM(ch_bams_from_input) ch_bams_from_input_lanemerged = MERGE_LANES_INPUTBAM.out.bam .join(MERGE_LANES_INPUTBAM.out.bai) + ch_flagstat_bams_from_input_lanemerged = MERGE_LANES_INPUTBAM.out.flagstat } else { - ch_bams_from_input_lanemerged = Channel.empty() - ch_flagstat_input_bam = Channel.empty() + ch_bams_from_input_lanemerged = Channel.empty() + ch_flagstat_bams_from_input_lanemerged = Channel.empty() } @@ -391,7 +392,7 @@ workflow EAGER { // ch_flagstat_for_endorspy_raw = MAP.out.flagstat - .mix( MERGE_LANES_INPUTBAM.out.flagstat ) + .mix( ch_flagstat_bams_from_input_lanemerged ) if (params.run_bamfiltering & !params.skip_deduplication) { ch_for_endorspy = ch_flagstat_for_endorspy_raw