Skip to content

Hisat2 #45

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Juke34 merged 3 commits into from
Feb 25, 2026
Merged

Hisat2 #45

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
47ad3ef
avoid mkfifo error du to /tmp not acccessible in singularity
Juke34 Feb 25, 2026
e1c5bf2
improve cache for check_aligner_params
Juke34 Feb 25, 2026
8c37cb9
update hisat2 for --temp-directory usage
Juke34 Feb 25, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion config/softwares.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
3 changes: 3 additions & 0 deletions modules/bash.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
14 changes: 12 additions & 2 deletions modules/hisat2.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -50,14 +52,22 @@ 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 \\
--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 {
"""
# 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 \\
--new-summary --summary-file ${fileName}_sorted_summary.txt --temp-directory \$TMPDIR \\
-p ${task.cpus} -x $index_basename -U $reads > ${fileName}.sam
"""
}
Expand Down