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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
40 lines
1.5 KiB
YAML
40 lines
1.5 KiB
YAML
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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