CI
b533a32bc8
Build pipeline: vsh-ci-template-7m7cc
Source commit: 73b07a96e0
Source message: Fix quotes in test (#4)
* Fix quotes in test
* query the first output file to pick up the 'name' value again and output it
grep with start and end position constaints
252 lines
6.5 KiB
YAML
252 lines
6.5 KiB
YAML
name: "bgzip"
|
|
version: "main"
|
|
argument_groups:
|
|
- name: "Inputs"
|
|
arguments:
|
|
- type: "file"
|
|
name: "--input"
|
|
description: "file to be compressed or decompressed"
|
|
info: null
|
|
must_exist: true
|
|
create_parent: true
|
|
required: true
|
|
direction: "input"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- name: "Outputs"
|
|
arguments:
|
|
- type: "file"
|
|
name: "--output"
|
|
description: "compressed or decompressed output"
|
|
info: null
|
|
must_exist: true
|
|
create_parent: true
|
|
required: true
|
|
direction: "output"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- type: "file"
|
|
name: "--index_name"
|
|
alternatives:
|
|
- "-I"
|
|
description: "name of BGZF index file [file.gz.gzi]"
|
|
info: null
|
|
must_exist: true
|
|
create_parent: true
|
|
required: false
|
|
direction: "output"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- name: "Arguments"
|
|
arguments:
|
|
- type: "integer"
|
|
name: "--offset"
|
|
alternatives:
|
|
- "-b"
|
|
description: "decompress at virtual file pointer (0-based uncompressed offset)"
|
|
info: null
|
|
required: false
|
|
direction: "input"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- type: "boolean_true"
|
|
name: "--decompress"
|
|
alternatives:
|
|
- "-d"
|
|
description: "decompress the input file"
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--rebgzip"
|
|
alternatives:
|
|
- "-g"
|
|
description: "use an index file to bgzip a file"
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--index"
|
|
alternatives:
|
|
- "-i"
|
|
description: "compress and create BGZF index"
|
|
info: null
|
|
direction: "input"
|
|
- type: "integer"
|
|
name: "--compress_level"
|
|
alternatives:
|
|
- "-l"
|
|
description: "compression level to use when compressing; 0 to 9, or -1 for default\
|
|
\ [-1]"
|
|
info: null
|
|
required: false
|
|
min: -1
|
|
max: 9
|
|
direction: "input"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- type: "boolean_true"
|
|
name: "--reindex"
|
|
alternatives:
|
|
- "-r"
|
|
description: "(re)index the output file"
|
|
info: null
|
|
direction: "input"
|
|
- type: "integer"
|
|
name: "--size"
|
|
alternatives:
|
|
- "-s"
|
|
description: "decompress INT bytes (uncompressed size)"
|
|
info: null
|
|
required: false
|
|
min: 0
|
|
direction: "input"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- type: "boolean_true"
|
|
name: "--test"
|
|
alternatives:
|
|
- "-t"
|
|
description: "test integrity of compressed file"
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--binary"
|
|
description: "Don't align blocks with text lines"
|
|
info: null
|
|
direction: "input"
|
|
resources:
|
|
- type: "bash_script"
|
|
path: "script.sh"
|
|
is_executable: true
|
|
description: "Block compression/decompression utility"
|
|
test_resources:
|
|
- type: "bash_script"
|
|
path: "test.sh"
|
|
is_executable: true
|
|
- type: "file"
|
|
path: "test_data"
|
|
info: null
|
|
status: "enabled"
|
|
requirements:
|
|
commands:
|
|
- "ps"
|
|
license: "MIT"
|
|
references:
|
|
doi:
|
|
- "10.1093/gigascience/giab007"
|
|
links:
|
|
repository: "https://github.com/samtools/htslib"
|
|
homepage: "https://www.htslib.org/"
|
|
documentation: "https://www.htslib.org/doc/bgzip.html"
|
|
runners:
|
|
- type: "executable"
|
|
id: "executable"
|
|
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
|
- type: "nextflow"
|
|
id: "nextflow"
|
|
directives:
|
|
tag: "$id"
|
|
auto:
|
|
simplifyInput: true
|
|
simplifyOutput: false
|
|
transcript: false
|
|
publish: false
|
|
config:
|
|
labels:
|
|
mem1gb: "memory = 1000000000.B"
|
|
mem2gb: "memory = 2000000000.B"
|
|
mem5gb: "memory = 5000000000.B"
|
|
mem10gb: "memory = 10000000000.B"
|
|
mem20gb: "memory = 20000000000.B"
|
|
mem50gb: "memory = 50000000000.B"
|
|
mem100gb: "memory = 100000000000.B"
|
|
mem200gb: "memory = 200000000000.B"
|
|
mem500gb: "memory = 500000000000.B"
|
|
mem1tb: "memory = 1000000000000.B"
|
|
mem2tb: "memory = 2000000000000.B"
|
|
mem5tb: "memory = 5000000000000.B"
|
|
mem10tb: "memory = 10000000000000.B"
|
|
mem20tb: "memory = 20000000000000.B"
|
|
mem50tb: "memory = 50000000000000.B"
|
|
mem100tb: "memory = 100000000000000.B"
|
|
mem200tb: "memory = 200000000000000.B"
|
|
mem500tb: "memory = 500000000000000.B"
|
|
mem1gib: "memory = 1073741824.B"
|
|
mem2gib: "memory = 2147483648.B"
|
|
mem4gib: "memory = 4294967296.B"
|
|
mem8gib: "memory = 8589934592.B"
|
|
mem16gib: "memory = 17179869184.B"
|
|
mem32gib: "memory = 34359738368.B"
|
|
mem64gib: "memory = 68719476736.B"
|
|
mem128gib: "memory = 137438953472.B"
|
|
mem256gib: "memory = 274877906944.B"
|
|
mem512gib: "memory = 549755813888.B"
|
|
mem1tib: "memory = 1099511627776.B"
|
|
mem2tib: "memory = 2199023255552.B"
|
|
mem4tib: "memory = 4398046511104.B"
|
|
mem8tib: "memory = 8796093022208.B"
|
|
mem16tib: "memory = 17592186044416.B"
|
|
mem32tib: "memory = 35184372088832.B"
|
|
mem64tib: "memory = 70368744177664.B"
|
|
mem128tib: "memory = 140737488355328.B"
|
|
mem256tib: "memory = 281474976710656.B"
|
|
mem512tib: "memory = 562949953421312.B"
|
|
cpu1: "cpus = 1"
|
|
cpu2: "cpus = 2"
|
|
cpu5: "cpus = 5"
|
|
cpu10: "cpus = 10"
|
|
cpu20: "cpus = 20"
|
|
cpu50: "cpus = 50"
|
|
cpu100: "cpus = 100"
|
|
cpu200: "cpus = 200"
|
|
cpu500: "cpus = 500"
|
|
cpu1000: "cpus = 1000"
|
|
debug: false
|
|
container: "docker"
|
|
engines:
|
|
- type: "docker"
|
|
id: "docker"
|
|
image: "quay.io/biocontainers/htslib:1.19--h81da01d_0"
|
|
target_registry: "images.viash-hub.com"
|
|
target_tag: "main"
|
|
namespace_separator: "/"
|
|
setup:
|
|
- type: "docker"
|
|
run:
|
|
- "bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\\s\\(.*\\)/bgzip: \"\\1\"\
|
|
/' > /var/software_versions.txt\n"
|
|
entrypoint: []
|
|
cmd: null
|
|
- type: "native"
|
|
id: "native"
|
|
build_info:
|
|
config: "src/bgzip/config.vsh.yaml"
|
|
runner: "executable"
|
|
engine: "docker|native"
|
|
output: "target/executable/bgzip"
|
|
executable: "target/executable/bgzip/bgzip"
|
|
viash_version: "0.9.0-RC6"
|
|
git_commit: "73b07a96e07de3b4429499795ef9fee678a96366"
|
|
git_remote: "https://github.com/viash-hub/toolbox"
|
|
package_config:
|
|
name: "toolbox"
|
|
version: "main"
|
|
description: "A collection of command-line tools.\n"
|
|
info: null
|
|
viash_version: "0.9.0-RC6"
|
|
source: "src"
|
|
target: "target"
|
|
config_mods:
|
|
- ".requirements.commands := ['ps']\n"
|
|
- ".engines += { type: \"native\" }"
|
|
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
|
- ".engines[.type == 'docker'].target_tag := 'main'"
|
|
keywords:
|
|
- "toolbox"
|
|
- "command-line"
|
|
- "tools"
|
|
license: "MIT"
|
|
organization: "vsh"
|
|
links:
|
|
repository: "https://github.com/viash-hub/toolbox"
|
|
issue_tracker: "https://github.com/viash-hub/toolbox/issues"
|