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rnaseq/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
CI 54557aa596 Build branch main with version main (fd0354d) 
Build pipeline: vsh-ci-template-w7zwh

Source commit: fd0354dae8

Source message: Point to new assets dir
2024-10-04 07:16:21 +00:00

329 lines
8.9 KiB
YAML
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name: "rsem_calculate_expression"
namespace: "rsem"
version: "main"
argument_groups:
- name: "Input"
arguments:
- type: "string"
name: "--id"
description: "Sample ID."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--strandedness"
description: "Sample strand-specificity. Must be one of unstranded, forward, reverse"
info: null
required: false
choices:
- "forward"
- "reverse"
- "unstranded"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--paired"
description: "Paired-end reads or not?"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--input"
description: "Input reads for quantification."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: true
multiple_sep: ","
- type: "file"
name: "--index"
description: "RSEM index."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_args"
description: "Extra rsem-calculate-expression arguments in addition to the defaults."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
name: "--counts_gene"
description: "Expression counts on gene level"
info: null
example:
- "sample.genes.results"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--counts_transcripts"
description: "Expression counts on transcript level"
info: null
example:
- "sample.isoforms.results"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--stat"
description: "RSEM statistics"
info: null
example:
- "sample.stat"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--logs"
description: "RSEM logs"
info: null
example:
- "sample.log"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bam_star"
description: "BAM file generated by STAR (optional)"
info: null
example:
- "sample.STAR.genome.bam"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bam_genome"
description: "Genome BAM file (optional)"
info: null
example:
- "sample.genome.bam"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bam_transcript"
description: "Transcript BAM file (optional)"
info: null
example:
- "sample.transcript.bam"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Calculate expression with RSEM.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "SRR6357070_1.fastq.gz"
- type: "file"
path: "SRR6357070_2.fastq.gz"
- type: "file"
path: "rsem.tar.gz"
info:
migration_info:
git_repo: "https://github.com/nf-core/rnaseq.git"
paths:
- "modules/nf-core/rsem/calculateexpression/main.nf"
- "modules/nf-core/rsem/calculateexpression/meta.yml"
last_sha: "92b2a7857de1dda9d1c19a088941fc81e2976ff7"
status: "enabled"
requirements:
commands:
- "ps"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
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: "ubuntu:22.04"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "build-essential"
- "gcc"
- "g++"
- "make"
- "wget"
- "zlib1g-dev"
- "unzip"
- "xxd"
- "perl"
- "r-base"
- "bowtie2"
- "python3-pip"
- "git"
interactive: false
- type: "docker"
run:
- "ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone\
\ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip\
\ && \\\nunzip ${STAR_VERSION}.zip && \\\ncd STAR-${STAR_VERSION}/source &&\
\ \\\nmake STARstatic CXXFLAGS_SIMD=-std=c++11 && \\\ncp STAR /usr/local/bin\
\ && \\\ncd /tmp && \\\nwget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_VERSION}.zip\
\ && \\\nunzip v${RSEM_VERSION}.zip && \\\ncd RSEM-${RSEM_VERSION} && \\\nmake\
\ && \\\nmake install && \\\nrm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip\
\ && \\\nrm -rf /tmp/RSEM-${RSEM_VERSION} /tmp/v${RSEM_VERSION}.zip && \\\n\
cd && \\\napt-get clean && \\\necho 'export PATH=$PATH:/usr/local/bin' >> /etc/profile\
\ && \\\necho 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \\\n/bin/bash\
\ -c \"source /etc/profile && source ~/.bashrc && echo $PATH && which STAR\"\
\n"
env:
- "STAR_VERSION=2.7.11b"
- "RSEM_VERSION=1.3.3"
- "TZ=Europe/Brussels"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/rsem/rsem_calculate_expression/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/rsem/rsem_calculate_expression"
executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
\ := '$id'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
organization: "vsh"
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