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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
1.6 KiB
YAML
47 lines
1.6 KiB
YAML
name: fgbio_fastqtobam
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description: |
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Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file
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keywords:
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- fastqtobam
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- fgbio
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tools:
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- fgbio:
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description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
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homepage: http://fulcrumgenomics.github.io/fgbio/
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documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
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tool_dev_url: https://github.com/fulcrumgenomics/fgbio
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doi: ""
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licence: ["MIT"]
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input:
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- reads:
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type: file
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description: pair of reads to be converted into BAM file
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pattern: "*.{fastq.gz}"
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- read_structure:
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type: string
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description: |
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A read structure should always be provided for each of the fastq files.
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If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string
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will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T").
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If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).
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https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.yml}"
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- umibam:
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type: file
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description: Converted, unsorted BAM file with RX tag reporting UMI sequence (if any)
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pattern: "*.{bam}"
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authors:
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- "@lescai"
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