CI
f36121ecc2
Build pipeline: viash-hub.toolbox.update-readme-hn4r8
Source commit: da8377a82e
Source message: update readme
90 lines
2.4 KiB
YAML
90 lines
2.4 KiB
YAML
name: bgzip
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description: Block compression/decompression utility
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links:
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homepage: https://www.htslib.org/
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documentation: https://www.htslib.org/doc/bgzip.html
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repository: https://github.com/samtools/htslib
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references:
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doi: 10.1093/gigascience/giab007
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license: MIT
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requirements:
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commands: [ bgzip ]
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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: file to be compressed or decompressed
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required: true
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- name: Outputs
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arguments:
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- name: --output
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type: file
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direction: output
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description: compressed or decompressed output
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required: true
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- name: --index_name
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alternatives: -I
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type: file
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direction: output
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description: name of BGZF index file [file.gz.gzi]
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- name: Arguments
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arguments:
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- name: --offset
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alternatives: -b
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type: integer
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description: decompress at virtual file pointer (0-based uncompressed offset)
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- name: --decompress
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alternatives: -d
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type: boolean_true
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description: decompress the input file
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- name: --rebgzip
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alternatives: -g
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type: boolean_true
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description: use an index file to bgzip a file
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- name: --index
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alternatives: -i
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type: boolean_true
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description: compress and create BGZF index
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- name: --compress_level
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alternatives: -l
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type: integer
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description: compression level to use when compressing; 0 to 9, or -1 for default [-1]
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min: -1
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max: 9
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- name: --reindex
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alternatives: -r
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type: boolean_true
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description: (re)index the output file
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- name: --size
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alternatives: -s
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type: integer
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description: decompress INT bytes (uncompressed size)
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min: 0
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- name: --test
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alternatives: -t
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type: boolean_true
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description: test integrity of compressed file
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- name: --binary
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type: boolean_true
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description: Don't align blocks with text lines
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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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- type: file
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path: test_data
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engines:
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- type: docker
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image: quay.io/biocontainers/htslib:1.19--h81da01d_0
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setup:
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- type: docker
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run: |
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bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
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runners:
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- type: executable
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- type: nextflow |