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36049bf544
* fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
43 lines
1.2 KiB
YAML
43 lines
1.2 KiB
YAML
name: fgbio_fastqtobam
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description: |
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Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads
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keywords:
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- fastqtobam
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- fgbio
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tools:
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- fgbio:
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description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
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homepage: http://fulcrumgenomics.github.io/fgbio/
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documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
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tool_dev_url: https://github.com/fulcrumgenomics/fgbio
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doi: ""
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licence: ["MIT"]
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input:
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- reads:
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type: file
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description: pair of reads to be converted into BAM file
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pattern: "*.{fastq.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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.yml}"
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- bam:
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type: file
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description: Unaligned, unsorted BAM file
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pattern: "*.{bam}"
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- cram:
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type: file
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description: Unaligned, unsorted CRAM file
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pattern: "*.{cram}"
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authors:
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- "@lescai"
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- "@matthdsm"
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