mirror of
https://github.com/MillironX/nf-core_modules.git
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Add Cell Ranger mkfastq, mkgtf, and count (#979)
* 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>
This commit is contained in:
parent
9d0cad583b
commit
e2ba70ed9a
20 changed files with 441 additions and 33 deletions
1
modules/cellranger/.gitignore
vendored
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modules/cellranger/.gitignore
vendored
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cellranger-*.tar.gz
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@ -4,7 +4,7 @@ LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>" \
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# Disclaimer: this container is not provided nor supported by 10x Genomics.
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# Disclaimer: this container is not provided nor supported by 10x Genomics.
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# Install procps and clean apt cache
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# Install procps and clean apt cache
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RUN apt-get update \
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RUN apt-get update --allow-releaseinfo-change \
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&& apt-get install -y procps \
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&& apt-get install -y procps \
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&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
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&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
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49
modules/cellranger/count/main.nf
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49
modules/cellranger/count/main.nf
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@ -0,0 +1,49 @@
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process CELLRANGER_COUNT {
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tag "$meta.gem"
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label 'process_high'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "nfcore/cellranger:6.0.2"
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input:
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tuple val(meta), path(reads)
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path reference
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output:
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path("sample-${meta.gem}/outs/*"), emit: outs
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def sample_arg = meta.samples.unique().join(",")
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def reference_name = reference.name
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"""
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cellranger \\
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count \\
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--id='sample-${meta.gem}' \\
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--fastqs=. \\
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--transcriptome=$reference_name \\
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--sample=$sample_arg \\
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--localcores=$task.cpus \\
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--localmem=${task.memory.toGiga()} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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stub:
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"""
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mkdir -p "sample-${meta.gem}/outs/"
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touch sample-${meta.gem}/outs/fake_file.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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}
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40
modules/cellranger/count/meta.yml
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modules/cellranger/count/meta.yml
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@ -0,0 +1,40 @@
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name: cellranger_count
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description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
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keywords:
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- align
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- count
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- reference
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tools:
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- cellranger:
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description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
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homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
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documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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doi: ""
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licence: 10x Genomics EULA
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- reference:
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type: folder
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description: Folder containing all the reference indices needed by Cell Ranger
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output:
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- outs:
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type: file
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description: Files containing the outputs of Cell Ranger
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pattern: "sample-${meta.gem}/outs/*"
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- versions:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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authors:
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- "@ggabernet"
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- "@Emiller88"
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31
modules/cellranger/mkfastq/main.nf
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31
modules/cellranger/mkfastq/main.nf
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process CELLRANGER_MKFASTQ {
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tag "mkfastq"
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label 'process_medium'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "litd/docker-cellranger:v6.1.1" // FIXME Add bcl2fastq to nf-core docker image
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input:
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path bcl
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path csv
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output:
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path "versions.yml", emit: versions
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path "*.fastq.gz" , emit: fastq
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script:
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def args = task.ext.args ?: ''
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"""
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cellranger mkfastq --id=${bcl.getSimpleName()} \
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--run=$bcl \
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--csv=$csv
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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}
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38
modules/cellranger/mkfastq/meta.yml
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38
modules/cellranger/mkfastq/meta.yml
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name: cellranger_mkfastq
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description: Module to create fastqs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.
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keywords:
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- reference
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- mkfastq
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- fastq
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- illumina
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- bcl2fastq
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tools:
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- cellranger:
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description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
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homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
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documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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doi: ""
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licence: 10x Genomics EULA
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input:
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- bcl:
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type: file
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description: Base call files
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pattern: "*.bcl.bgzf"
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- csv:
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type: file
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description: Sample sheet
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pattern: "*.csv"
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output:
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- fastq:
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type: file
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description: Unaligned FastQ files
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pattern: "*.fastq.gz"
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- versions:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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authors:
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- "@ggabernet"
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- "@Emiller88"
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- "@RHReynolds"
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31
modules/cellranger/mkgtf/main.nf
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31
modules/cellranger/mkgtf/main.nf
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process CELLRANGER_MKGTF {
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tag "$gtf"
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label 'process_low'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
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}
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container "nfcore/cellranger:6.0.2"
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input:
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path gtf
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output:
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path "*.filtered.gtf", emit: gtf
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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"""
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cellranger \\
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mkgtf \\
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$gtf \\
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${gtf.baseName}.filtered.gtf \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
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END_VERSIONS
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"""
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}
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31
modules/cellranger/mkgtf/meta.yml
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31
modules/cellranger/mkgtf/meta.yml
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name: cellranger_mkgtf
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description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
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keywords:
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- reference
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- mkref
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- index
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tools:
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- cellranger:
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description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
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homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
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documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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doi: ""
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licence: 10x Genomics EULA
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input:
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- gtf:
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type: file
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description:
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pattern: "*.gtf"
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output:
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- gtf:
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type: folder
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description: gtf transcriptome file
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pattern: "*.filtered.gtf"
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- versions:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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authors:
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- "@ggabernet"
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- "@Emiller88"
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@ -1,39 +1,37 @@
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name: cellranger_mkref
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name: cellranger_mkref
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description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
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description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
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keywords:
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keywords:
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- reference
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- reference
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- mkref
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- mkref
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- index
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- index
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tools:
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tools:
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- cellranger:
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- cellranger:
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description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
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description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
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homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
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homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
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documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
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doi: ""
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doi: ""
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licence: 10x Genomics EULA
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licence: 10x Genomics EULA
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input:
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input:
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- fasta:
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- fasta:
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type: file
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type: file
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description: fasta genome file
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description: fasta genome file
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pattern: "*.{fasta,fa}"
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pattern: "*.{fasta,fa}"
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- gtf:
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- gtf:
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type: file
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type: file
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description: gtf transcriptome file
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description: gtf transcriptome file
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pattern: "*.gtf"
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pattern: "*.gtf"
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- reference_name:
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- reference_name:
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type: val
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type: val
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description: name to give the reference folder
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description: name to give the reference folder
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pattern: str
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pattern: str
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output:
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output:
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- versions:
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- reference:
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type: file
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type: folder
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description: File containing software version
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description: Folder containing all the reference indices needed by Cell Ranger
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pattern: "versions.yml"
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- versions:
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- reference:
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type: file
|
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type: folder
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description: File containing software version
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description: Folder containing all the reference indices needed by Cell Ranger
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pattern: "versions.yml"
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authors:
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authors:
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- "@ggabernet"
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- "@ggabernet"
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@ -270,9 +270,25 @@ cat/fastq:
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- modules/cat/fastq/**
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- modules/cat/fastq/**
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- tests/modules/cat/fastq/**
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- tests/modules/cat/fastq/**
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cellranger/mkref:
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cellranger/gtf: # &cellranger/gtf
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- modules/cellranger/gtf/**
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- tests/modules/cellranger/gtf/**
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cellranger/mkref: # &cellranger/mkref
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- modules/cellranger/mkref/**
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- modules/cellranger/mkref/**
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- tests/modules/cellranger/mkref/**
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- tests/modules/cellranger/mkref/**
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# - *cellranger/gtf
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- modules/cellranger/gtf/**
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- tests/modules/cellranger/gtf/**
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cellranger/count:
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- modules/cellranger/count/**
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- tests/modules/cellranger/count/**
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# - *cellranger/mkref
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- modules/cellranger/mkref/**
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- tests/modules/cellranger/mkref/**
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- modules/cellranger/gtf/**
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- tests/modules/cellranger/gtf/**
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checkm/lineagewf:
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checkm/lineagewf:
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- modules/checkm/lineagewf/**
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- modules/checkm/lineagewf/**
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33
tests/modules/cellranger/count/main.nf
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33
tests/modules/cellranger/count/main.nf
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@ -0,0 +1,33 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CELLRANGER_MKGTF } from '../../../../modules/cellranger/mkgtf/main.nf'
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include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf'
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include { CELLRANGER_COUNT } from '../../../../modules/cellranger/count/main.nf'
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workflow test_cellranger_count {
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input = [ [ id:'test', single_end:true, strandedness:'forward', gem: '123', samples: ["test_10x"] ], // meta map
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||||||
|
[ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
|
||||||
|
file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
]
|
||||||
|
|
||||||
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
||||||
|
reference_name = "homo_sapiens_chr22_reference"
|
||||||
|
|
||||||
|
CELLRANGER_MKGTF ( gtf )
|
||||||
|
|
||||||
|
CELLRANGER_MKREF (
|
||||||
|
fasta,
|
||||||
|
CELLRANGER_MKGTF.out.gtf,
|
||||||
|
reference_name
|
||||||
|
)
|
||||||
|
|
||||||
|
CELLRANGER_COUNT(
|
||||||
|
input,
|
||||||
|
CELLRANGER_MKREF.out.reference
|
||||||
|
)
|
||||||
|
}
|
31
tests/modules/cellranger/count/nextflow.config
Normal file
31
tests/modules/cellranger/count/nextflow.config
Normal file
|
@ -0,0 +1,31 @@
|
||||||
|
process {
|
||||||
|
|
||||||
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||||
|
|
||||||
|
withName: CELLRANGER_MKGTF {
|
||||||
|
ext.args = '--attribute=gene_biotype:protein_coding \
|
||||||
|
--attribute=gene_biotype:lincRNA \
|
||||||
|
--attribute=gene_biotype:antisense \
|
||||||
|
--attribute=gene_biotype:IG_LV_gene \
|
||||||
|
--attribute=gene_biotype:IG_V_gene \
|
||||||
|
--attribute=gene_biotype:IG_V_pseudogene \
|
||||||
|
--attribute=gene_biotype:IG_D_gene \
|
||||||
|
--attribute=gene_biotype:IG_J_gene \
|
||||||
|
--attribute=gene_biotype:IG_J_pseudogene \
|
||||||
|
--attribute=gene_biotype:IG_C_gene \
|
||||||
|
--attribute=gene_biotype:IG_C_pseudogene \
|
||||||
|
--attribute=gene_biotype:TR_V_gene \
|
||||||
|
--attribute=gene_biotype:TR_V_pseudogene \
|
||||||
|
--attribute=gene_biotype:TR_D_gene \
|
||||||
|
--attribute=gene_biotype:TR_J_gene \
|
||||||
|
--attribute=gene_biotype:TR_J_pseudogene \
|
||||||
|
--attribute=gene_biotype:TR_C_gene'
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: CELLRANGER_COUNT {
|
||||||
|
ext.args = '--chemistry SC3Pv3'
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
19
tests/modules/cellranger/count/test.yml
Normal file
19
tests/modules/cellranger/count/test.yml
Normal file
|
@ -0,0 +1,19 @@
|
||||||
|
- name: cellranger count test_cellranger_count
|
||||||
|
command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config
|
||||||
|
tags:
|
||||||
|
- cellranger
|
||||||
|
- cellranger/count
|
||||||
|
files:
|
||||||
|
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
|
||||||
|
- path: output/cellranger/sample-123/outs/metrics_summary.csv
|
||||||
|
md5sum: 707df0f101d479d93f412ca74f9c4131
|
||||||
|
- path: output/cellranger/sample-123/outs/molecule_info.h5
|
||||||
|
md5sum: cf03b2b3ca776a1c37aa3518e91268ba
|
||||||
|
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
|
||||||
|
md5sum: 15441da9cfceea0bb48c8b66b1b860df
|
||||||
|
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
|
||||||
|
md5sum: 7c3d49c77016a09535aff61a027f750c
|
||||||
|
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
|
||||||
|
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
|
||||||
|
md5sum: 40c8df814eb8723b7317b234dc8222e9
|
||||||
|
- path: output/cellranger/sample-123/outs/web_summary.html
|
26
tests/modules/cellranger/mkfastq/main.nf
Normal file
26
tests/modules/cellranger/mkfastq/main.nf
Normal file
|
@ -0,0 +1,26 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { UNTAR } from '../../../../modules/untar/main.nf'
|
||||||
|
include { CELLRANGER_MKFASTQ } from '../../../../modules/cellranger/mkfastq/main.nf'
|
||||||
|
|
||||||
|
workflow test_cellranger_mkfastq_simple {
|
||||||
|
|
||||||
|
simple_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true)
|
||||||
|
tiny_bcl = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true)
|
||||||
|
|
||||||
|
UNTAR ( tiny_bcl )
|
||||||
|
|
||||||
|
CELLRANGER_MKFASTQ ( UNTAR.out.untar, simple_csv)
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_cellranger_mkfastq_illumina {
|
||||||
|
|
||||||
|
samplesheet_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true)
|
||||||
|
tiny_bcl = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true)
|
||||||
|
|
||||||
|
UNTAR ( tiny_bcl )
|
||||||
|
|
||||||
|
CELLRANGER_MKFASTQ ( UNTAR.out.untar, samplesheet_csv)
|
||||||
|
}
|
5
tests/modules/cellranger/mkfastq/nextflow.config
Normal file
5
tests/modules/cellranger/mkfastq/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
||||||
|
process {
|
||||||
|
|
||||||
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||||
|
|
||||||
|
}
|
13
tests/modules/cellranger/mkfastq/test.yml
Normal file
13
tests/modules/cellranger/mkfastq/test.yml
Normal file
|
@ -0,0 +1,13 @@
|
||||||
|
- name: cellranger mkfastq test_cellranger_mkfastq_simple
|
||||||
|
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config
|
||||||
|
tags:
|
||||||
|
- cellranger
|
||||||
|
- cellranger/mkfastq
|
||||||
|
# files:
|
||||||
|
# - path: output/cellranger/genome.filtered.gtf
|
||||||
|
# md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
|
||||||
|
- name: cellranger mkfastq test_cellranger_mkfastq_illumina
|
||||||
|
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config
|
||||||
|
tags:
|
||||||
|
- cellranger
|
||||||
|
- cellranger/mkfastq
|
11
tests/modules/cellranger/mkgtf/main.nf
Normal file
11
tests/modules/cellranger/mkgtf/main.nf
Normal file
|
@ -0,0 +1,11 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { CELLRANGER_MKGTF } from '../../../../modules/cellranger/mkgtf/main.nf'
|
||||||
|
|
||||||
|
workflow test_cellranger_mkgtf {
|
||||||
|
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
|
||||||
|
|
||||||
|
CELLRANGER_MKGTF ( gtf )
|
||||||
|
}
|
27
tests/modules/cellranger/mkgtf/nextflow.config
Normal file
27
tests/modules/cellranger/mkgtf/nextflow.config
Normal file
|
@ -0,0 +1,27 @@
|
||||||
|
process {
|
||||||
|
|
||||||
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||||
|
|
||||||
|
withName: CELLRANGER_MKGTF {
|
||||||
|
ext.args = '--attribute=gene_biotype:protein_coding \
|
||||||
|
--attribute=gene_biotype:lincRNA \
|
||||||
|
--attribute=gene_biotype:antisense \
|
||||||
|
--attribute=gene_biotype:IG_LV_gene \
|
||||||
|
--attribute=gene_biotype:IG_V_gene \
|
||||||
|
--attribute=gene_biotype:IG_V_pseudogene \
|
||||||
|
--attribute=gene_biotype:IG_D_gene \
|
||||||
|
--attribute=gene_biotype:IG_J_gene \
|
||||||
|
--attribute=gene_biotype:IG_J_pseudogene \
|
||||||
|
--attribute=gene_biotype:IG_C_gene \
|
||||||
|
--attribute=gene_biotype:IG_C_pseudogene \
|
||||||
|
--attribute=gene_biotype:TR_V_gene \
|
||||||
|
--attribute=gene_biotype:TR_V_pseudogene \
|
||||||
|
--attribute=gene_biotype:TR_D_gene \
|
||||||
|
--attribute=gene_biotype:TR_J_gene \
|
||||||
|
--attribute=gene_biotype:TR_J_pseudogene \
|
||||||
|
--attribute=gene_biotype:TR_C_gene'
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
8
tests/modules/cellranger/mkgtf/test.yml
Normal file
8
tests/modules/cellranger/mkgtf/test.yml
Normal file
|
@ -0,0 +1,8 @@
|
||||||
|
- name: cellranger mkgtf test_cellranger_mkgtf
|
||||||
|
command: nextflow run tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c tests/config/nextflow.config -c tests/modules/cellranger/mkgtf/nextflow.config
|
||||||
|
tags:
|
||||||
|
- cellranger
|
||||||
|
- cellranger/mkgtf
|
||||||
|
files:
|
||||||
|
- path: output/cellranger/genome.filtered.gtf
|
||||||
|
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
|
Loading…
Reference in a new issue