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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>
47 lines
1.3 KiB
YAML
47 lines
1.3 KiB
YAML
name: umitools_extract
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description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
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keywords:
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- umitools
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- extract
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tools:
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- umi_tools:
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description: >
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UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)
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and single cell RNA-Seq cell barcodes
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documentation: https://umi-tools.readthedocs.io/en/latest/
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license: ["MIT"]
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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: list
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description: |
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List of input FASTQ files whose UMIs will be extracted.
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output:
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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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Extracted FASTQ files. |
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For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. |
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For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
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pattern: "*.{fastq.gz}"
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- log:
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type: file
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description: Logfile for umi_tools
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pattern: "*.{log}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@drpatelh"
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- "@grst"
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