CI
fbf20cbd8a
Build pipeline: vsh-ci-build-template-d9jmw
Source commit: d87d344d4e
Source message: Merge pull request #5 from viash-hub/update-test-resources
update test data
199 lines
5.2 KiB
YAML
199 lines
5.2 KiB
YAML
name: "mapping_and_qc"
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version: "main"
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argument_groups:
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- name: "Input arguments"
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arguments:
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- type: "file"
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name: "--input_r1"
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--input_r2"
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--reference"
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info: null
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Output arguments"
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arguments:
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- type: "file"
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name: "--multiqc_output"
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info: null
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example:
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- "multiqc.html"
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must_exist: true
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create_parent: true
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required: true
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direction: "output"
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multiple: false
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multiple_sep: ";"
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resources:
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- type: "nextflow_script"
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path: "main.nf"
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is_executable: true
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entrypoint: "run_wf"
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description: "Run STAR and QC"
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info: null
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status: "enabled"
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requirements:
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commands:
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- "ps"
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dependencies:
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- name: "cutadapt"
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repository:
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type: "vsh"
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repo: "vsh/biobox"
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tag: "main"
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- name: "falco"
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repository:
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type: "vsh"
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repo: "vsh/biobox"
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tag: "main"
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- name: "multiqc"
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repository:
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type: "vsh"
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repo: "vsh/biobox"
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tag: "main"
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- name: "star/star_align_reads"
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repository:
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type: "vsh"
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repo: "vsh/biobox"
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tag: "main"
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- name: "samtools/samtools_stats"
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repository:
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type: "vsh"
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repo: "vsh/biobox"
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tag: "main"
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repositories:
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- type: "vsh"
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name: "bb"
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repo: "vsh/biobox"
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tag: "main"
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license: "MIT"
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links:
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repository: "https://github.com/viash-hub/playground"
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runners:
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- type: "nextflow"
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id: "nextflow"
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directives:
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tag: "$id"
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auto:
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simplifyInput: true
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simplifyOutput: false
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transcript: false
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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debug: false
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container: "docker"
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engines:
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- type: "native"
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id: "native"
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- type: "native"
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id: "native"
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build_info:
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config: "src/mapping_and_qc/config.vsh.yaml"
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runner: "nextflow"
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engine: "native|native"
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output: "target/nextflow/mapping_and_qc"
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executable: "target/nextflow/mapping_and_qc/main.nf"
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viash_version: "0.9.0-RC6"
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git_commit: "d87d344d4e46dc6f938e57a009607946ed31447c"
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git_remote: "https://github.com/viash-hub/playground"
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dependencies:
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- "target/dependencies/vsh/vsh/biobox/main/nextflow/cutadapt"
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- "target/dependencies/vsh/vsh/biobox/main/nextflow/falco"
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- "target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc"
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- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
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- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
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package_config:
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name: "playground"
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version: "main"
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description: "A collection of bioinformatics pipelines to illustrate the use of\
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\ biobox (and biotools).\n"
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info: null
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viash_version: "0.9.0-RC6"
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source: "src"
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target: "target"
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config_mods:
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- ".requirements.commands := ['ps']\n"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'main'"
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keywords:
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- "bioinformatics"
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- "sequence"
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- "high-throughput"
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- "mapping"
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- "counting"
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- "pipeline"
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license: "MIT"
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organization: "vsh"
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links:
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repository: "https://github.com/viash-hub/playground"
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issue_tracker: "https://github.com/viash-hub/playground/issues"
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