From 47ad3ef40d84f37efcdceabbec697e655d4fa5a4 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Wed, 25 Feb 2026 10:13:51 +0100 Subject: [PATCH 1/3] avoid mkfifo error du to /tmp not acccessible in singularity --- modules/hisat2.nf | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/modules/hisat2.nf b/modules/hisat2.nf index 8124255..d06c5b1 100644 --- a/modules/hisat2.nf +++ b/modules/hisat2.nf @@ -26,6 +26,8 @@ process hisat2 { label 'hisat2' tag "${meta.uid}" publishDir "${params.outdir}/${outpath}", pattern: "*.txt", mode: 'copy' + // use a local tmp + scratch true input: tuple val(meta), path(reads) @@ -50,12 +52,20 @@ process hisat2 { // alignment if (meta.paired) { """ + # To avoid /tmp not mounted in Singularity container + export TMPDIR=\$PWD/tmp + mkdir -p \$TMPDIR + hisat2 ${hisat2_options} --novel-splicesite-outfile ${fileName}_splicesite.txt \\ --new-summary --summary-file ${fileName}_sorted_summary.txt \\ -p ${task.cpus} -x $index_basename -1 ${reads[0]} -2 ${reads[1]} > ${fileName}.sam """ } else { """ + # To avoid /tmp not mounted in Singularity container + export TMPDIR=\$PWD/tmp + mkdir -p \$TMPDIR + hisat2 ${hisat2_options} --novel-splicesite-outfile ${fileName}_splicesite.txt \\ --new-summary --summary-file ${fileName}_sorted_summary.txt \\ -p ${task.cpus} -x $index_basename -U $reads > ${fileName}.sam From e1c5bf2ea90059d017b72846e0689f06796a3625 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Wed, 25 Feb 2026 10:15:09 +0100 Subject: [PATCH 2/3] improve cache for check_aligner_params --- modules/bash.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/bash.nf b/modules/bash.nf index c84a985..2d35604 100644 --- a/modules/bash.nf +++ b/modules/bash.nf @@ -187,6 +187,9 @@ process check_aligner_params{ tag "${meta.uid}" publishDir "${params.outdir}/${outpath}", pattern: "*.txt", mode: 'copy' + // improve cache + cache 'lenient' // or 'deep' depending needs + input: tuple val(meta), path(fastq) val aligner_list From 8c37cb96cd0f01f272c3387231af945437220f1b Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Wed, 25 Feb 2026 10:34:36 +0100 Subject: [PATCH 3/3] update hisat2 for --temp-directory usage --- config/softwares.config | 2 +- modules/hisat2.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/softwares.config b/config/softwares.config index 2b568cf..6151fb4 100644 --- a/config/softwares.config +++ b/config/softwares.config @@ -27,7 +27,7 @@ process { container = 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0' } withLabel: 'hisat2' { - container = 'quay.io/biocontainers/hisat2:2.2.1--hdbdd923_6' + container = 'quay.io/biocontainers/hisat2:2.2.2--h503566f_0' } withLabel: 'kallisto' { container = 'quay.io/biocontainers/kallisto:0.48.0--h0d531b0_1' diff --git a/modules/hisat2.nf b/modules/hisat2.nf index d06c5b1..845326c 100644 --- a/modules/hisat2.nf +++ b/modules/hisat2.nf @@ -57,7 +57,7 @@ process hisat2 { mkdir -p \$TMPDIR hisat2 ${hisat2_options} --novel-splicesite-outfile ${fileName}_splicesite.txt \\ - --new-summary --summary-file ${fileName}_sorted_summary.txt \\ + --new-summary --summary-file ${fileName}_sorted_summary.txt --temp-directory \$TMPDIR \\ -p ${task.cpus} -x $index_basename -1 ${reads[0]} -2 ${reads[1]} > ${fileName}.sam """ } else { @@ -67,7 +67,7 @@ process hisat2 { mkdir -p \$TMPDIR hisat2 ${hisat2_options} --novel-splicesite-outfile ${fileName}_splicesite.txt \\ - --new-summary --summary-file ${fileName}_sorted_summary.txt \\ + --new-summary --summary-file ${fileName}_sorted_summary.txt --temp-directory \$TMPDIR \\ -p ${task.cpus} -x $index_basename -U $reads > ${fileName}.sam """ }