From 46b3c445de2339aa1125f25655b73bb0215caa42 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Mon, 5 Jun 2023 15:04:12 +0200
Subject: [PATCH] subworkflows/local/hicstuff_sub.nf: remove some unused import
and rename the SAMTOOLS_SORT process
---
subworkflows/local/hicstuff_sub.nf | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index 3f49999..f4ace14 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -9,8 +9,7 @@ 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 { SAMTOOLS_SORT as SAMTOOLS_SORT1} from '../../modules/nf-core/custom/samtools/sort/main'
-include { SAMTOOLS_SORT as SAMTOOLS_SORT2} from '../../modules/nf-core/custom/samtools/sort/main'
+include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
include { FILTER_PAIR } from '../../modules/nf-core/custom/filterbam/main'
include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
@@ -67,13 +66,13 @@ workflow HICSTUFF_SUB {
error "Error: filter_pcr and filter_pcr_picard can't both be true at the same time! Set one of them false in the config file"
}
else if (params.filter_pcr_picard){
- SAMTOOLS_SORT1(
+ SAMTOOLS_SORT(
BOWTIE2_ALIGNMENT.out.bam
)
PICARD_MARKDUPLICATES(
- SAMTOOLS_SORT1.out.bam,
+ SAMTOOLS_SORT.out.bam,
fasta.collect(),
index.collect()
)
--
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