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4b8c7ac7bd
* added template for module * update main * added specific code * wrong variable name in else script * added tests for both split and nosplit * docker test successful - updating yaml * adding echo to version print
55 lines
1.5 KiB
YAML
55 lines
1.5 KiB
YAML
name: samtools_bam2fq
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description: |
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The module uses bam2fq method 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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- inputbam:
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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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- split:
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type: boolean
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description: |
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TRUE/FALSE value to indicate if reads should be separated into
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/1, /2 and if present other, or singleton.
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Note: choosing TRUE will generate 4 different files.
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Choosing FALSE will produce a single file, which will be interleaved in case
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the input contains paired reads.
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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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- 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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- 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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authors:
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- "@lescai"
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