mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
e2ba70ed9a
* feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
31 lines
836 B
Text
31 lines
836 B
Text
process CELLRANGER_MKFASTQ {
|
|
tag "mkfastq"
|
|
label 'process_medium'
|
|
|
|
if (params.enable_conda) {
|
|
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
|
|
}
|
|
container "litd/docker-cellranger:v6.1.1" // FIXME Add bcl2fastq to nf-core docker image
|
|
|
|
input:
|
|
path bcl
|
|
path csv
|
|
|
|
output:
|
|
path "versions.yml", emit: versions
|
|
path "*.fastq.gz" , emit: fastq
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
cellranger mkfastq --id=${bcl.getSimpleName()} \
|
|
--run=$bcl \
|
|
--csv=$csv
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|