nf-core_modules/modules/cellranger/mkref/main.nf
Regina Hertfelder Reynolds 1b24005f07
Add bcl2fastq2 to cellranger dockerfile (#1115)
* refactor: add bcl2fastq to cellranger dockerfile

bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.

* chore: add bcl2fastq zip to .gitignore

* style: fix code linting error

* test(cellranger): Add tiles to mkfastq

* additional dockerfile for mkfastq

* update readme and dockerfiles

* update readme

* fix: update container for mkfastq

* docs: correct typos in readme

* test: update md5sum following cellranger update

* test: update md5sum following cellranger update

* fix: new line for external args in mkfastq

* test: update mkfastq tiles argument

* test: comment out mkfastq tests until smaller test data found

* test: stub-run mkfastq test until smaller test data found

* test: fix incorrect file path for mkfastq

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 19:58:22 +01:00

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process CELLRANGER_MKREF {
tag 'mkref'
label 'process_high'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.1.2"
input:
path fasta
path gtf
val reference_name
output:
path "${reference_name}", emit: reference
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
"""
cellranger \\
mkref \\
--genome=$reference_name \\
--fasta=$fasta \\
--genes=$gtf
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
"""
}