Build branch add-labels with version add-labels (89519f6)
Build pipeline: viash-hub.rnaseq.add-labels-lln98
Source commit: 89519f6e38
Source message: Add labels configuration
This commit is contained in:
537
target/executable/workflows/post_processing/.config.vsh.yaml
Normal file
537
target/executable/workflows/post_processing/.config.vsh.yaml
Normal file
@@ -0,0 +1,537 @@
|
||||
name: "post_processing"
|
||||
namespace: "workflows"
|
||||
version: "add-labels"
|
||||
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: "string"
|
||||
name: "--strandedness"
|
||||
description: "Sample strand-specificity. Must be one of unstranded, forward, reverse\
|
||||
\ or auto"
|
||||
info: null
|
||||
default:
|
||||
- "auto"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--paired"
|
||||
description: "Paired fastq files or not?"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fasta"
|
||||
description: "Path to FASTA genome file."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--fai"
|
||||
description: "Path to FASTA index"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
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: "--genome_bam"
|
||||
description: "Genome BAM file"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--chrom_sizes"
|
||||
description: "File containing chromosome lengths"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--star_multiqc"
|
||||
description: "STAR align log file."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_picard_args"
|
||||
description: "Extra arguments to pass to picard MarkDuplicates command in addition\
|
||||
\ to defaults defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- ""
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_stringtie_args"
|
||||
description: "Extra arguments to pass to stringtie command in addition to defaults\
|
||||
\ defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- ""
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--stringtie_ignore_gtf"
|
||||
description: "Perform reference-guided de novo assembly of transcripts using StringTie,\
|
||||
\ i.e. don't restrict to those in GTF file."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_bedtools_args"
|
||||
description: "Extra arguments to pass to bedtools genomecov command in addition\
|
||||
\ to defaults defined by the pipeline."
|
||||
info: null
|
||||
default:
|
||||
- ""
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--bam_csi_index"
|
||||
description: "Create a CSI index for BAM files instead of the traditional BAI\
|
||||
\ index. This will be required for genomes with larger chromosome sizes."
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--min_mapped_reads"
|
||||
description: "Minimum percentage of uniquely mapped reads below which samples\
|
||||
\ are removed from further processing."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--with_umi"
|
||||
description: "Enable UMI-based read deduplication."
|
||||
info: null
|
||||
default:
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--skip_qc"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--skip_markduplicates"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--skip_stringtie"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--skip_bigwig"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--processed_genome_bam"
|
||||
info: null
|
||||
default:
|
||||
- "$id.genome.bam"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--genome_bam_index"
|
||||
info: null
|
||||
default:
|
||||
- "$id.genome.bam.bai"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--genome_bam_stats"
|
||||
info: null
|
||||
default:
|
||||
- "$id.genome.stats"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--genome_bam_flagstat"
|
||||
info: null
|
||||
default:
|
||||
- "$id.genome.flagstat"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--genome_bam_idxstats"
|
||||
info: null
|
||||
default:
|
||||
- "$id.genome.idxstats"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--markduplicates_metrics"
|
||||
info: null
|
||||
default:
|
||||
- "$id.MarkDuplicates.metrics.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--stringtie_transcript_gtf"
|
||||
info: null
|
||||
default:
|
||||
- "$id.stringtie.transcripts.gtf"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--stringtie_coverage_gtf"
|
||||
info: null
|
||||
default:
|
||||
- "$id.stringtie.coverage.gtf"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--stringtie_abundance"
|
||||
info: null
|
||||
default:
|
||||
- "$id.stringtie.gene_abundance.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--stringtie_ballgown"
|
||||
info: null
|
||||
default:
|
||||
- "$id.stringtie.ballgown"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bedgraph_forward"
|
||||
info: null
|
||||
default:
|
||||
- "$id.forward.bedgraph"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bedgraph_reverse"
|
||||
info: null
|
||||
default:
|
||||
- "$id.reverse.bedgraph"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bigwig_forward"
|
||||
info: null
|
||||
default:
|
||||
- "$id.forward.bigwig"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--bigwig_reverse"
|
||||
info: null
|
||||
default:
|
||||
- "$id.reverse.bigwig"
|
||||
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"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "A viash sub-workflow for the post-processing stage of nf-core/rnaseq\
|
||||
\ pipeline.\n"
|
||||
info: null
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
dependencies:
|
||||
- name: "picard_markduplicates"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "samtools/samtools_sort"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_index"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_stats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_flagstat"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_idxstats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- name: "stringtie"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "bedtools_genomecov"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "ucsc/bedclip"
|
||||
repository:
|
||||
type: "local"
|
||||
- name: "ucsc/bedgraphtobigwig"
|
||||
repository:
|
||||
type: "local"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
tag: "v0.1.0"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "midmem"
|
||||
- "midcpu"
|
||||
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"
|
||||
script:
|
||||
- "includeConfig(\"nextflow_labels.config\")"
|
||||
debug: false
|
||||
container: "docker"
|
||||
engines:
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/workflows/post_processing/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "native"
|
||||
output: "target/executable/workflows/post_processing"
|
||||
executable: "target/executable/workflows/post_processing/post_processing"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
|
||||
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/picard_markduplicates"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
|
||||
- "target/nextflow/stringtie"
|
||||
- "target/nextflow/bedtools_genomecov"
|
||||
- "target/nextflow/ucsc/bedclip"
|
||||
- "target/nextflow/ucsc/bedgraphtobigwig"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "add-labels"
|
||||
info:
|
||||
test_resources:
|
||||
- path: "gs://viash-hub-test-data/rnaseq/v1"
|
||||
dest: "testData"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "main"
|
||||
- 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.resources += {path: '/src/workflows/utils/labels.config',\
|
||||
\ dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].directives.tag\
|
||||
\ := '$id'\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
|
||||
)'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'add-labels'"
|
||||
organization: "vsh"
|
||||
Reference in New Issue
Block a user