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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>
52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
name: bismark_deduplicate
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description: |
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Removes alignments to the same position in the genome
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from the Bismark mapping output.
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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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licence: ["GPL-3.0-or-later"]
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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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- bam:
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type: file
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description: BAM file containing read alignments
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pattern: "*.{bam}"
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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: Deduplicated output BAM file containing read alignments
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pattern: "*.{deduplicated.bam}"
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- report:
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type: file
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description: Bismark deduplication reports
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pattern: "*.{deduplication_report.txt}"
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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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- "@phue"
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