From 09e19d2d8dbfe3dcfe3d49e2ee82aa2c4aef7625 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Thu, 1 Jun 2023 16:26:10 +0200
Subject: [PATCH] correct path of markduplicates
---
subworkflows/local/hicstuff_sub.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index 92c5181..ad0332d 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -8,7 +8,7 @@ include { BUILD_MATRIX_COOL_ALT } from '../../modules/local/hicstuff/build_matri
include { FILTER_EVENT } from '../../modules/local/hicstuff/filter_event'
include { DISTANCE_LAW } from '../../modules/local/hicstuff/distance_law'
include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr'
-include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/gatk4/markduplicates/main'
+include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/markduplicates/main'
include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
@@ -89,7 +89,7 @@ workflow HICSTUFF_SUB {
.map {
meta1, bam1, meta2, bam2 ->
meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null
- },
+ }.view(),
FRAGMENT_ENZYME.out.info_contigs.collect(),
digestion,
fasta.collect()
--
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