From aac64942b4e36c2f64dded6596d616a008bd7b8e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 13 Sep 2018 17:58:55 +0200
Subject: [PATCH] Kallisto.nf: update report format
---
src/nf_modules/Kallisto/mapping_paired.nf | 4 ++--
src/nf_modules/Kallisto/mapping_single.nf | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/Kallisto/mapping_paired.nf b/src/nf_modules/Kallisto/mapping_paired.nf
index 15718373..4f4ad3d1 100644
--- a/src/nf_modules/Kallisto/mapping_paired.nf
+++ b/src/nf_modules/Kallisto/mapping_paired.nf
@@ -27,10 +27,10 @@ process mapping_fastq {
script:
"""
-mkdir ${reads[0].baseName}
+mkdir ${pair_id}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
+${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
"""
}
diff --git a/src/nf_modules/Kallisto/mapping_single.nf b/src/nf_modules/Kallisto/mapping_single.nf
index cba5aff2..97861e76 100644
--- a/src/nf_modules/Kallisto/mapping_single.nf
+++ b/src/nf_modules/Kallisto/mapping_single.nf
@@ -36,7 +36,7 @@ mkdir ${file_id}
kallisto quant -i ${index} -t ${task.cpus} --single \
--bias --bootstrap-samples 100 -o ${file_id} \
-l ${params.mean} -s ${params.sd} \
-${reads} > ${file_id}_kallisto_report.txt
+${reads} &> ${file_id}/kallisto_report.txt
"""
}
--
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