vsh/rnaseq
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
3e6bb670c56a9ccb3dcd2c9fe00b4627b873bdc1
rnaseq/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
CI 3e6bb670c5 Build branch v0.1 with version v0.1.1 (0f49a3f) 
Build pipeline: vsh-ci-dev-w9454

Source commit: 0f49a3ff62

Source message: Bump version to v0.1.1
2024-10-17 17:31:01 +00:00

317 lines
8.2 KiB
YAML
Raw Blame History

name: "pseudo_alignment_and_quant"
namespace: "workflows"
version: "v0.1.1"
argument_groups:
- name: "Input"
arguments:
- type: "string"
name: "--id"
description: "ID of the sample."
info: null
example:
- "foo"
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastq_1"
alternatives:
- "-i"
description: "Path to the sample (or read 1 of paired end sample)."
info: null
example:
- "input.fastq.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastq_2"
description: "Path to read 2 of the sample."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--strandedness"
description: "Sample strand-specificity. Must be one of unstranded, forward, or\
\ reverse"
info: null
required: false
choices:
- "forward"
- "reverse"
- "unstranded"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--gtf"
description: "GTF file"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--transcript_fasta"
description: "Fasta file of the reference transcriptome."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--pseudo_aligner"
description: "Specifies the pseudo aligner to use - available options are 'salmon'.\
\ Runs in addition to '--aligner'."
info: null
default:
- "false"
required: false
choices:
- "salmon"
- "kallisto"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--salmon_index"
description: "Salmon index"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--kallisto_index"
description: "Kallisto index"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--lib_type"
description: "Override library type inferred based on strandedness defined in\
\ meta object"
info: null
default:
- ""
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--kallisto_quant_fragment_length"
description: "For single-end mode only, the estimated average fragment length\
\ to use for quantification with Kallisto."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--kallisto_quant_fragment_length_sd"
description: "For single-end mode only, the estimated standard deviation of the\
\ fragment length for quantification with Kallisto."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
name: "--pseudo_multiqc"
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--quant_out_dir"
info: null
default:
- "$id.quant"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--salmon_quant_results_file"
info: null
default:
- "$id.quant.sf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--kallisto_quant_results_file"
info: null
default:
- "$id.abundance.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "nextflow_script"
path: "main.nf"
is_executable: true
entrypoint: "run_wf"
description: "A viash sub-workflow for pseudo alignment and quantification stage of\
\ nf-core/rnaseq pipeline.\n"
info: null
status: "enabled"
requirements:
commands:
- "ps"
dependencies:
- name: "salmon/salmon_quant"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "kallisto/kallisto_quant"
repository:
type: "local"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$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: "native"
id: "native"
build_info:
config: "src/workflows/pseudo_alignment_and_quant/config.vsh.yaml"
runner: "executable"
engine: "native"
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"
package_config:
name: "rnaseq"
version: "v0.1.1"
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 := 'v0.1.1'"
organization: "vsh"
Reference in New Issue View Git Blame Copy Permalink