From 2fde78ba219959000d5dbdd51834ee0bf49d5529 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 22 Feb 2021 13:51:15 +0100
Subject: [PATCH] picard: improve picard index output
---
src/nf_modules/picard/main.nf | 2 +-
src/nf_modules/samtools/main.nf | 1 -
2 files changed, 1 insertion(+), 2 deletions(-)
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
index 8a9b0d8a..f47aadef 100644
--- a/src/nf_modules/picard/main.nf
+++ b/src/nf_modules/picard/main.nf
@@ -39,7 +39,7 @@ process index_fasta {
"""
PicardCommandLine CreateSequenceDictionary \
REFERENCE=${fasta} \
-OUTPUT=${fasta.simpleName}.dict
+OUTPUT=${fasta.baseName}.dict
"""
}
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index d778e31f..9599ec63 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -181,7 +181,6 @@ process merge_multi_bam {
samtools merge -@ ${task.cpus} \
${bams[0].simpleName}_merged.bam \
${bams}
-
"""
}
--
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