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* 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>
33 lines
1.1 KiB
Text
33 lines
1.1 KiB
Text
#!/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),
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file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
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reference_name = "homo_sapiens_chr22_reference"
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CELLRANGER_MKGTF ( gtf )
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CELLRANGER_MKREF (
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fasta,
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CELLRANGER_MKGTF.out.gtf,
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reference_name
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)
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CELLRANGER_COUNT(
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input,
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CELLRANGER_MKREF.out.reference
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)
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}
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