CI
aa043fdc19
Build pipeline: viash-hub.biobox.qualimap-6tqq7
Source commit: 28cd122935
Source message: Merge branch 'main' into qualimap
79 lines
1.9 KiB
YAML
79 lines
1.9 KiB
YAML
name: seqtk_subseq
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namespace: seqtk
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description: |
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Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a name.lst (sequence ids file) or a reg.bed (genomic regions file).
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keywords: [subseq, FASTA, FASTQ]
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links:
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repository: https://github.com/lh3/seqtk/tree/v1.4
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license: MIT
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authors:
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- __merge__: /src/_authors/theodoro_gasperin.yaml
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roles: [ author, maintainer ]
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argument_groups:
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- name: Inputs
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arguments:
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- name: "--input"
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type: file
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direction: input
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description: The input FASTA/Q file.
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required: true
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example: input.fa
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- name: "--name_list"
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type: file
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direction: input
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description: |
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List of sequence names (name.lst) or genomic regions (reg.bed) to extract.
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required: true
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example: list.lst
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- name: Outputs
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arguments:
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- name: "--output"
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alternatives: -o
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type: file
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direction: output
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description: The output FASTA/Q file.
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required: true
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default: output.fa
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- name: Options
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arguments:
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- name: "--tab"
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alternatives: -t
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type: boolean_true
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description: TAB delimited output.
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- name: "--strand_aware"
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alternatives: -s
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type: boolean_true
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description: Strand aware.
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- name: "--sequence_line_length"
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alternatives: -l
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type: integer
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description: |
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Sequence line length of input fasta file. Default: 0.
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example: 0
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resources:
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- type: bash_script
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path: script.sh
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test_resources:
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- type: bash_script
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path: test.sh
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engines:
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- type: docker
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image: quay.io/biocontainers/seqtk:1.4--he4a0461_2
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setup:
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- type: docker
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run: |
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echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/software_versions.txt
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runners:
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- type: executable
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- type: nextflow
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