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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>
52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
name: ivar_trim
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description: Trim primer sequences rom a BAM file with iVar
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keywords:
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- amplicon sequencing
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- trimming
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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: Co-ordinate sorted BAM file
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pattern: "*.bam"
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- bai:
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type: file
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description: Index file for co-ordinate sorted BAM file
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pattern: "*.bai"
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- bed:
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type: file
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description: BED file with primer labels and positions
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pattern: "*.bed"
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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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- bam:
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type: file
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description: iVar generated trimmed bam file (unsorted)
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pattern: "*.bam"
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- log:
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type: file
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description: Log file generated by iVar for use with MultiQC
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pattern: "*.log"
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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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