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ee46c19d03
* add Picard FastqToSam * Update test.yml * update tests * possible fix? * fixed! * Update modules/picard/fastqtosam/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Update modules/picard/fastqtosam/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * simplify tests * fix tests * revert version check Co-authored-by: CMGG ICT Team <ict@cmgg.be> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
46 lines
1.2 KiB
YAML
46 lines
1.2 KiB
YAML
name: "picard_fastqtosam"
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description: Converts a FASTQ file to an unaligned BAM or SAM file.
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keywords:
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- fastq
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- unaligned
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- bam
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tools:
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- picard:
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description: |
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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
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data and formats such as SAM/BAM/CRAM and VCF.
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homepage: https://broadinstitute.github.io/picard/
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documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard-
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tool_dev_url: https://github.com/broadinstitute/picard
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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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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#
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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: Unaligned bam file
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pattern: "*.{bam}"
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authors:
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- "@matthdsm"
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