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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>
50 lines
1.7 KiB
YAML
Executable file
50 lines
1.7 KiB
YAML
Executable file
name: sequenzautils_bam2seqz
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description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
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keywords:
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- bam2seqz
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tools:
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- sequenzautils:
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description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
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homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html
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documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html
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doi: 10.1093/annonc/mdu479
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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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- normalbam:
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type: file
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description: BAM file from the reference/normal sample
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pattern: "*.{bam}"
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- tumourbam:
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type: file
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description: BAM file from the tumour sample
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: Reference FASTA file
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pattern: "*.{fasta}"
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- wigfile:
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type: file
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description: GC content wiggle file
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pattern: "*.{wig.gz}"
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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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- seqz:
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type: file
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description: Seqz file
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pattern: "*.{seqz.gz}"
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authors:
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- "@kaurravneet4123"
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