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691feeafdc
* fasta_fai_dict tuple is now split into separate input channels * fix: lint errors * fix: pytest errors * Update modules/gatk4/splitncigarreads/meta.yml * Update modules/gatk4/splitncigarreads/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
48 lines
1.5 KiB
YAML
48 lines
1.5 KiB
YAML
name: gatk4_splitncigarreads
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description: Splits reads that contain Ns in their cigar string
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keywords:
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- vcf
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- merge
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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licence: ['Apache-2.0']
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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']
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- bam:
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type: list
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description: BAM/SAM/CRAM file containing reads
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pattern: "*.{bam,sam,cram}"
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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output:
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- bam:
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type: file
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description: Output file with split reads (BAM/SAM/CRAM)
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pattern: "*.{bam,sam,cram}"
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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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authors:
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- "@kevinmenden"
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