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https://github.com/MillironX/nf-core_modules.git
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bb90e4fb78
* Remove customisation from bcftools modules * Add save_mpileup option to bcftools/mpileup * Remove params.save_mpileup from ivar/consensus * Update meta.ymls
56 lines
1.7 KiB
YAML
56 lines
1.7 KiB
YAML
name: ivar_consensus
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description: Generate a consensus sequence from a BAM file using iVar
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keywords:
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- amplicon sequencing
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- consensus
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- fasta
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tools:
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- ivar:
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description: |
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iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
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homepage: https://github.com/andersen-lab/ivar
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documentation: https://andersen-lab.github.io/ivar/html/manualpage.html
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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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- bam:
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type: file
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description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file
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pattern: "*.bam"
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- fasta:
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type: file
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description: The reference sequence used for mapping and generating the BAM file
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pattern: "*.fa"
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- save_mpileup:
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type: boolean
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description: Save mpileup file generated by ivar consensus
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patter: "*.mpileup"
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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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- fasta:
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type: file
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description: iVar generated consensus sequence
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pattern: "*.fa"
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- qual:
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type: file
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description: iVar generated quality file
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pattern: "*.qual.txt"
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- mpileup:
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type: file
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description: mpileup output from samtools mpileup [OPTIONAL]
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pattern: "*.mpileup"
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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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- "@andersgs"
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- "@drpatelh"
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