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* Samtools fixmate module * Update modules/samtools/fixmate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf * Update modules/samtools/fixmate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update meta.yml Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
49 lines
1.6 KiB
YAML
49 lines
1.6 KiB
YAML
name: samtools_fixmate
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description: Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.
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keywords:
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- fixmate
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- samtools
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- insert size
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- repair
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- bam
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- paired
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- read pairs
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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: http://www.htslib.org/doc/samtools.html
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tool_dev_url: https://github.com/samtools/samtools
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doi: 10.1093/bioinformatics/btp352
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licence: ['MIT']
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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, must be sorted by name, not coordinate
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pattern: "*.{bam,cram,sam}"
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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/CRAM/SAM file with mate information added and/or proper pairs recalled
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pattern: "*.{bam,cram,sam}"
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authors:
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- "@sppearce"
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