From d5cf091f1a6b542413f6b9f5926c394142db84f4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 28 Feb 2022 14:59:20 +0100
Subject: [PATCH] src/nf_modules/hisat2/main.nf
---
.../hisat2/2.2.1/docker_init.sh | 4 +--
src/nf_modules/hisat2/main.nf | 27 +++++++++++--------
2 files changed, 18 insertions(+), 13 deletions(-)
diff --git a/src/.docker_modules/hisat2/2.2.1/docker_init.sh b/src/.docker_modules/hisat2/2.2.1/docker_init.sh
index 11a1df82..adeffb7e 100755
--- a/src/.docker_modules/hisat2/2.2.1/docker_init.sh
+++ b/src/.docker_modules/hisat2/2.2.1/docker_init.sh
@@ -1,5 +1,5 @@
#!/bin/sh
docker pull lbmc/hisat2:2.2.1
-# docker build src/.docker_modules/hisat2/2.1.1 -t 'lbmc/hisat2:2.2.1'
-# docker push lbmc/hisat2:2.2.1
+docker build src/.docker_modules/hisat2/2.2.1 -t 'lbmc/hisat2:2.2.1'
+docker push lbmc/hisat2:2.2.1
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/hisat2:2.2.1" --push src/.docker_modules/hisat2/2.2.1
diff --git a/src/nf_modules/hisat2/main.nf b/src/nf_modules/hisat2/main.nf
index 96c53239..34492a11 100644
--- a/src/nf_modules/hisat2/main.nf
+++ b/src/nf_modules/hisat2/main.nf
@@ -1,5 +1,5 @@
version = "2.2.1"
-container_url = "lbmc/histat2:${version}"
+container_url = "lbmc/hisat2:${version}"
params.index_fasta = ""
params.index_fasta_out = ""
@@ -20,12 +20,13 @@ process index_fasta {
script:
"""
+gunzip ${fasta}
hisat2-build -p ${task.cpus} \
- ${fasta} \
+ ${fasta.baseName} \
${fasta.simpleName} &> \
${fasta.simpleName}_hisat2_index_report.txt
-if grep -q "Error" ${fasta.simpleName}_bowtie2_index_report.txt; then
+if grep -q "Error" ${fasta.simpleName}_hisat2_index_report.txt; then
exit 1
fi
"""
@@ -70,30 +71,34 @@ process mapping_fastq {
if (reads.size() == 2)
"""
- histat2 ${params.mapping_fastq} \
+ hisat2 ${params.mapping_fastq} \
-p ${task.cpus} \
-x ${index_id} \
-1 ${reads[0]} \
-2 ${reads[1]} 2> \
${file_prefix}_ht2_mapping_report_tmp.txt \
- | samtools view -@ ${task.cpus} -bS - \
- | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam -
+ | samtools view -@ ${task.cpus} -bS - 2>> \
+ ${file_prefix}_ht2_mapping_report_tmp.txt \
+ | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
+ ${file_prefix}_ht2_mapping_report.txt
- if grep -q "Error" ${file_prefix}_ht2_mapping_report_tmp.txt; then
+ if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1
fi
"""
else
"""
- histat2 ${params.mapping_fastq} \
+ hisat2 ${params.mapping_fastq} \
-p ${task.cpus} \
-x ${index_id} \
-U ${reads} 2> \
${file_prefix}_ht2_mapping_report_tmp.txt \
- | samtools view -@ ${task.cpus} -bS - \
- | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam -
+ | samtools view -@ ${task.cpus} -bS - 2>> \
+ ${file_prefix}_ht2_mapping_report.txt \
+ | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
+ ${file_prefix}_ht2_mapping_report.txt
- if grep -q "Error" ${file_prefix}_ht2_mapping_report_tmp.txt; then
+ if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1
fi
"""
--
GitLab