From 988c40208d299faeec9f4f63c504fe29763c13f1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 27 Jan 2021 14:21:15 +0100
Subject: [PATCH] picard: fix bams var in main.nf
---
src/nf_modules/picard/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
index 47ba54b6..0faec2e0 100644
--- a/src/nf_modules/picard/main.nf
+++ b/src/nf_modules/picard/main.nf
@@ -19,9 +19,9 @@ process mark_duplicate {
PicardCommandLine MarkDuplicates \
VALIDATION_STRINGENCY=LENIENT \
REMOVE_DUPLICATES=true \
- INPUT=${bams[0]} \
- OUTPUT=${bams[0].baseName}_dedup.bam \
- METRICS_FILE=${bams[0].baseName}_picard_dedup_report.txt &> \
- picard_${bams[0].baseName}.log
+ INPUT=${bam} \
+ OUTPUT=${bam.baseName}_dedup.bam \
+ METRICS_FILE=${bam.baseName}_picard_dedup_report.txt &> \
+ picard_${bam.baseName}.log
"""
}
--
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