2020-08-07 14:11:31 +00:00
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name: samtools_flagstat
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description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
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keywords:
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- stats
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- mapping
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- counts
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- bam
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- sam
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- cram
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: hhttp://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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2020-10-15 10:13:54 +00:00
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- enable_conda:
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2020-08-07 14:11:31 +00:00
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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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/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- bai:
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type: file
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description: Index for BAM/CRAM/SAM file
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pattern: "*.{bai,crai,sai}"
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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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- flagstat:
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type: file
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description: File containing samtools flagstat output
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pattern: "*.{flagstat}"
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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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- "@drpatelh"
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