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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
56 lines
1.7 KiB
YAML
56 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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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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- 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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- save_mpileup:
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type: boolean
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description: Save mpileup file generated by ivar variants
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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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- 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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- 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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