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* Add atlas/splitmerge module * Finish the tests for atlas/splitmerge * Prettier * Update modules/atlas/splitmerge/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Remove curly brackets from meta.yml parameters For single-file outputs, as reviewed * Lintung: Remove trailing white-space Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
70 lines
2 KiB
YAML
70 lines
2 KiB
YAML
name: "atlas_splitmerge"
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description: split single end read groups by length and merge paired end reads
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keywords:
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- split
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- merge
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- bam
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- read group
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tools:
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- "atlas":
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description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
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homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
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documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
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tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
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doi: "10.1101/105346"
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licence: "['GPL v3']"
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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: Single input BAM file.
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pattern: "*.bam"
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- bai:
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type: file
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description: The BAI file for the input BAM file
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pattern: "*.bai"
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- read_group_setting:
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type: file
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description: |
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TXT file containing the split and merge settings for
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each readgroup. Each line consist of one readgroup,
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single/double identifier and the maximum cycle number
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of the sequencer. e.g. "RG1 single 100"
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pattern: "*.txt"
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- blacklist:
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type: file
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description: |
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blacklist.txt (optional), A txt file with blacklisted read names
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that should be ignored and just written to file, each on a new line
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pattern: "*.txt"
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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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- bam:
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type: file
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description: A BAM file with suffix_mergedReads.bam
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pattern: "*_mergedReads.bam"
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- filelist:
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type: file
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description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz
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pattern: "*.txt.gz"
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authors:
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- "@merszym"
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