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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>
37 lines
1.4 KiB
YAML
37 lines
1.4 KiB
YAML
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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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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- fasta:
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type: file
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description: fasta genome file
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pattern: "*.{fasta,fa}"
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- gtf:
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type: file
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description: gtf transcriptome file
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pattern: "*.gtf"
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- reference_name:
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type: val
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description: name to give the reference folder
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pattern: str
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output:
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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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- 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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