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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
51 lines
1.7 KiB
YAML
51 lines
1.7 KiB
YAML
name: ivar_variants
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description: Call variants from a BAM file using iVar
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keywords:
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- amplicon sequencing
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- variants
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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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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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- gff:
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type: file
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description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
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patter: "*.gff"
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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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- tsv:
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type: file
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description: iVar generated TSV file with the variants
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pattern: "*.tsv"
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@andersgs"
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- "@drpatelh"
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