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8a2f01c416
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * Add bwa samse * Fix container paths * remove TODO comment * Updated based on code from from @grst on bwa/sampe * Clarify output docs
59 lines
1.4 KiB
YAML
59 lines
1.4 KiB
YAML
name: bwa_samse
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description: Convert bwa SA coordinate file to SAM format
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keywords:
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- bwa
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- aln
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- short-read
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- align
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- reference
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- fasta
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- map
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- sam
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- bam
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tools:
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- bwa:
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description: |
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BWA is a software package for mapping DNA sequences against
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a large reference genome, such as the human genome.
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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://bio-bwa.sourceforge.net/
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doi: "10.1093/bioinformatics/btp324"
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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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- reads:
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type: file
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description: FASTQ files specified alongside meta in input channel.
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pattern: "*.{fastq,fq}.gz"
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- sai:
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type: file
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description: SAI file specified alongside meta and reads in input channel.
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pattern: "*.sai"
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- index:
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type: directory
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description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
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pattern: "bwa/"
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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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- 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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- bam:
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type: file
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description: BAM file
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pattern: "*.bam"
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authors:
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- "@jfy133"
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