From f2f617c5518479021a7a6aaebc05282c0ea05c1c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 5 May 2021 14:41:17 +0200
Subject: [PATCH] nf_modules: update alntools awk
---
src/nf_modules/alntools/main.nf | 4 ++--
src/nf_modules/kb/main.nf | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/alntools/main.nf b/src/nf_modules/alntools/main.nf
index 148e976b..a302ec2d 100644
--- a/src/nf_modules/alntools/main.nf
+++ b/src/nf_modules/alntools/main.nf
@@ -21,14 +21,14 @@ process bam2ec {
script:
"""
-awk -F"[\\t;]" '
+awk -F"[\t;]" '
\$3=="exon" {
ID=gensub(/transcript_id \"(.*)\"/, "\\1", "g", \$11);
LEN[ID]+=\$5-\$4+1;
}
END{
for(i in LEN)
- {print i"\\t"LEN[i]}
+ {print i"\t"LEN[i]}
}
' ${gtf} > ${gtf.simpleName}_transcripts_lengths.tsv
alntools bam2ec ${params.bam2ec} -t ${gtf.simpleName}_transcripts_lengths.tsv -c 8 ${bam} ${bam.simpleName}.bin
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index d174b19c..e5895ba6 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -102,7 +102,7 @@ workflow count {
switch(params.kb_protocol) {
case "marsseq":
split(fastq, config)
- kb_marseq(index, split.out.fastq.view(), transcript_to_gene, whitelist_optional)
+ kb_marseq(index.collect(), split.out.fastq.view(), transcript_to_gene, whitelist_optional)
kb_marseq.out.counts.set{res_counts}
kb_marseq.out.report.set{res_report}
break;
--
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