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f9ce8664ba
* add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
58 lines
1.7 KiB
YAML
58 lines
1.7 KiB
YAML
name: bismark_align
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description: Performs alignment of BS-Seq reads using bismark
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keywords:
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- bismark
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- 3-letter genome
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- map
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- bam
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tools:
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- bismark:
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description: |
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Bismark is a tool to map bisulfite treated sequencing reads
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and perform methylation calling in a quick and easy-to-use fashion.
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homepage: https://github.com/FelixKrueger/Bismark
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documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
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doi: 10.1093/bioinformatics/btr167
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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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- index:
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type: dir
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description: Bismark genome index directory
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pattern: "BismarkIndex"
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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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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- unmapped:
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type: file
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description: Output FastQ file(s) containing unmapped reads
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pattern: "*.{fq.gz}"
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- report:
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type: file
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description: Bismark alignment reports
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pattern: "*{report.txt}"
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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.txt}"
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authors:
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- "@phue"
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