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48 lines
1.2 KiB
YAML
48 lines
1.2 KiB
YAML
name: samtools_collatefastq
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description: |
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The module uses collate and then fastq methods from samtools to
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convert a SAM, BAM or CRAM file to FASTQ format
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keywords:
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- bam2fq
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- samtools
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- fastq
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tools:
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- samtools:
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description: Tools for dealing with SAM, BAM and CRAM files
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homepage: None
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documentation: http://www.htslib.org/doc/1.1/samtools.html
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tool_dev_url: None
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doi: ""
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licence: ["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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- input:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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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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FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
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or a single interleaved .fq.gz file if the user chooses not to split the reads.
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pattern: "*.fq.gz"
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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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- "@lescai"
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- "@maxulysse"
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