Build branch main with version main (cf97972)
Build pipeline: viash-hub.htrnaseq.main-6f8s8
Source commit: cf9797232d
Source message: WIP: add component to parse STAR logs (#7)
* WIP: add component to parse STAR logs
* Add tests and logging
This commit is contained in:
214
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
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214
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
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name: "combine_star_logs"
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namespace: "stats"
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version: "main"
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argument_groups:
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- name: "Arguments"
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arguments:
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- type: "string"
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name: "--barcodes"
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description: "Barcodes responding to the respective log files.\n"
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info: null
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required: false
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- type: "file"
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name: "--star_logs"
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description: "Paths to the STAR log files (most frequently called Log.final.out)\n"
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info: null
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example:
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- "Log.final.out"
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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: "input"
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multiple: true
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multiple_sep: ";"
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- type: "file"
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name: "--gene_summary_logs"
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description: "Paths to the Summary.csv files from the STAR Solo output. Can be\
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\ found in\nthe 'Solo.out/Gene' folder relative to the root of the STAR output\
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\ directory. \n"
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info: null
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example:
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- "Summary.txt"
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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: "input"
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multiple: true
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multiple_sep: ";"
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- type: "file"
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name: "--reads_per_gene_logs"
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description: "Paths to the 'ReadsPerGene.out.tab' files as output by STAR.\n"
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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: false
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- type: "file"
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name: "--output"
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description: "Tab-delimited file describing for each barcode (as the rows), the\
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\ metrics (as columns)\ngathered from the different input files. \n"
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info: null
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default:
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- "starLogs.txt"
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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: "python_script"
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path: "script.py"
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is_executable: true
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- type: "file"
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path: "nextflow_labels.config"
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dest: "nextflow_labels.config"
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test_resources:
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- type: "python_script"
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path: "test.py"
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is_executable: true
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- type: "file"
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path: "test_data"
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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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license: "MIT"
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links:
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repository: "https://github.com/viash-hub/htrnaseq"
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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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script:
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- "includeConfig(\"nextflow_labels.config\")"
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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: "python:3.12-slim"
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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: "apt"
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packages:
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- "procps"
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interactive: false
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- type: "python"
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user: false
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packages:
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- "pandas"
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upgrade: true
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test_setup:
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- type: "python"
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user: false
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packages:
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- "viashpy"
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upgrade: true
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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/stats/combine_star_logs/config.vsh.yaml"
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runner: "nextflow"
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engine: "docker|native"
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output: "target/nextflow/stats/combine_star_logs"
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executable: "target/nextflow/stats/combine_star_logs/main.nf"
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viash_version: "0.9.0-RC7"
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git_commit: "cf9797232db1306bfd5696287928cababe317d99"
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git_remote: "https://x-access-token:ghs_KjB7pWu8DQM3iFulLu7RI06qnt5K8S1A0eaE@github.com/viash-hub/htrnaseq"
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package_config:
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name: "htrnaseq"
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version: "main"
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description: "High-throughput pipeline [WIP]\n"
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info: null
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viash_version: "0.9.0-RC7"
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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'].config.script\
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\ := 'includeConfig(\"nextflow_labels.config\")'\n.resources += {path: '/src/config/labels.config',\
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\ dest: 'nextflow_labels.config'}\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/htrnaseq"
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issue_tracker: "https://github.com/viash-hub/htrnaseq/issues"
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