CI
14e0d12189
Build pipeline: viash-hub.rnaseq.main-b6jtr
Source commit: ce40a4a6d9
Source message: add unit tests
268 lines
6.7 KiB
YAML
268 lines
6.7 KiB
YAML
name: "deseq2_qc"
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version: "main"
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argument_groups:
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- name: "input"
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arguments:
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- type: "file"
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name: "--counts"
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description: "Count file matrix where rows are genes and columns are samples."
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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: "boolean"
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name: "--vst"
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description: "Use vst transformation instead of rlog with .DESeq2"
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info: null
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default:
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- false
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "integer"
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name: "--count_col"
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description: "First column containing sample count data."
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info: null
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default:
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- 3
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "integer"
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name: "--id_col"
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description: "Column containing identifiers to be used."
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info: null
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default:
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- 1
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--sample_suffix"
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description: "Suffix to remove after sample name in columns e.g. '.rmDup.bam'\
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\ if 'DRUG_R1.rmDup.bam'."
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info: null
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default:
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- ""
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--outprefix"
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description: "Output prefix"
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info: null
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default:
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- "deseq2"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--label"
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description: "Label to used in MultiQC report"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Output"
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arguments:
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- type: "file"
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name: "--outdir"
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info: null
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default:
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- "deseq2"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--pca_multiqc"
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info: null
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default:
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- "deseq2.pca.vals_mqc.tsv"
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must_exist: true
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--sample_dists_multiqc"
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info: null
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default:
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- "deseq2.sample.dists_mqc.tsv"
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must_exist: true
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create_parent: true
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required: false
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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: "r_script"
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path: "script.r"
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is_executable: true
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- type: "file"
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path: "deseq2_pca_header.txt"
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- type: "file"
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path: "deseq2_clustering_header.txt"
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description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\
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\ in the counts files\n"
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test_resources:
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- type: "bash_script"
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path: "test.sh"
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is_executable: true
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- type: "file"
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path: "counts.tsv"
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info:
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migration_info:
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git_repo: "https://github.com/nf-core/rnaseq.git"
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paths:
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- "modules/local/deseq2_qc.nf"
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last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
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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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repositories:
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- type: "vsh"
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name: "biobox"
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repo: "vsh/biobox"
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tag: "main"
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- type: "vsh"
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name: "craftbox"
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repo: "craftbox"
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tag: "v0.1.0"
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runners:
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- type: "executable"
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id: "executable"
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docker_setup_strategy: "ifneedbepullelsecachedbuild"
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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: "docker"
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id: "docker"
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image: "rocker/r2u:22.04"
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target_registry: "images.viash-hub.com"
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target_tag: "main"
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namespace_separator: "/"
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setup:
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- type: "r"
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cran:
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- "optparse"
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- "ggplot2"
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- "RColorBrewer"
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- "pheatmap"
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- "stringr"
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- "matrixStats"
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bioc:
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- "DESeq2"
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bioc_force_install: false
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/deseq2_qc/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/deseq2_qc"
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executable: "target/executable/deseq2_qc/deseq2_qc"
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viash_version: "0.9.0"
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git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
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git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
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package_config:
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name: "rnaseq"
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version: "main"
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info:
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test_resources:
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- path: "gs://viash-hub-test-data/rnaseq/v1"
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dest: "testData"
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repositories:
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- type: "vsh"
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name: "biobox"
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repo: "vsh/biobox"
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tag: "main"
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- type: "vsh"
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name: "craftbox"
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repo: "craftbox"
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tag: "v0.1.0"
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viash_version: "0.9.0"
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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.runners[.type == 'nextflow'].directives.tag\
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\ := '$id'\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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organization: "vsh"
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