Build branch main with version main (65dd41d)
Build pipeline: viash-hub.htrnaseq.main-vhms8
Source commit: 65dd41d8b1
Source message: Optimize spawning of processes
This commit is contained in:
199
target/executable/eset/create_pdata/.config.vsh.yaml
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199
target/executable/eset/create_pdata/.config.vsh.yaml
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name: "create_pdata"
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namespace: "eset"
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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: "file"
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name: "--star_stats_file"
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description: "Tab-delimited text file containing statistics (per column) that\
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\ were generated\nfrom the STAR log files (Log.final.out, Summary.csv, ReadsPerGene.out.tab).\n\
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Each entry (row) in the file describes the values for one well (barcode).\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: 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: "--nrReadsNrGenesPerChromPool"
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description: "Pivot table in tsv format of the combined nrReadsNrGenesPerChrom\
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\ files from STAR. \nDescribes per chromosome (as columns) the number of reads,\
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\ as well as the total number \nof reads per cell barcode and the percentage\
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\ of nuclear, ERCC and mitochondrial\nreads.\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: 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: "--output"
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info: null
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default:
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- "pData.$id.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: "create_pdata.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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description: "Create a pdata file by combining the mapping statistics \n"
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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: "nrReadsNrGenesPerChromPool.txt"
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- type: "file"
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path: "starLogs.txt"
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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/eset/create_pdata/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/eset/create_pdata"
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executable: "target/executable/eset/create_pdata/create_pdata"
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viash_version: "0.9.0"
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git_commit: "65dd41d8b1b4a307735c72320c96c0880c75f17f"
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git_remote: "https://x-access-token:ghs_McZDF0yobnnHmOEb2Q4JaaB3pzr9mz1VbIOs@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:
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test_resources:
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- path: "gs://viash-hub-test-data/htrnaseq/v1/"
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dest: "resources_test"
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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'].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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1173
target/executable/eset/create_pdata/create_pdata
Executable file
1173
target/executable/eset/create_pdata/create_pdata
Executable file
File diff suppressed because it is too large
Load Diff
105
target/executable/eset/create_pdata/nextflow_labels.config
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105
target/executable/eset/create_pdata/nextflow_labels.config
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@@ -0,0 +1,105 @@
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executor {
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$k8s {
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submitRateLimit = '10sec'
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pollInterval = '1 sec'
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}
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}
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process {
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container = 'nextflow/bash:latest'
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// default resources
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memory = { 8.Gb * task.attempt }
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cpus = 8
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maxForks = 36
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// Retry for exit codes that have something to do with memory issues
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errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
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maxRetries = 3
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maxMemory = 192.GB
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// Resource labels
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withLabel: verylowcpu { cpus = 2 }
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withLabel: lowcpu { cpus = 8 }
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withLabel: midcpu { cpus = 16 }
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withLabel: highcpu { cpus = 32 }
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withLabel: verylowmem { memory = { get_memory( 4.GB * task.attempt ) } }
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withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
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withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
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withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
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}
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profiles {
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// detect tempdir
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tempDir = java.nio.file.Paths.get(
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System.getenv('NXF_TEMP') ?:
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System.getenv('VIASH_TEMP') ?:
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System.getenv('TEMPDIR') ?:
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System.getenv('TMPDIR') ?:
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'/tmp'
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).toAbsolutePath()
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mount_temp {
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docker.temp = tempDir
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podman.temp = tempDir
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charliecloud.temp = tempDir
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}
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no_publish {
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process {
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withName: '.*' {
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publishDir = [
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enabled: false
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]
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}
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}
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}
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docker {
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docker.fixOwnership = true
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docker.enabled = true
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// docker.userEmulation = true
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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}
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local {
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// This config is for local processing.
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process {
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maxMemory = 25.GB
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withLabel: verylowcpu { cpus = 2 }
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withLabel: lowcpu { cpus = 4 }
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withLabel: midcpu { cpus = 6 }
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withLabel: highcpu { cpus = 12 }
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withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
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withLabel: midmem { memory = { get_memory( 12.GB * task.attempt ) } }
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withLabel: highmem { memory = { get_memory( 20.GB * task.attempt ) } }
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}
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}
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}
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def get_memory(to_compare) {
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if (!process.containsKey("maxMemory") || !process.maxMemory) {
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return to_compare
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}
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try {
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if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
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return process.maxMemory
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}
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else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
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return max_memory as nextflow.util.MemoryUnit
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}
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else {
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return to_compare
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}
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} catch (all) {
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println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
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System.exit(1)
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}
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}
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