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b5d3a795da663b4721668553ce8c44a784d1f529
rnaseq/target/executable/workflows/pre_processing/.config.vsh.yaml
CI b5d3a795da Build branch add-labels with version add-labels (e244fcf) 
Build pipeline: viash-hub.rnaseq.add-labels-n4fx6

Source commit: e244fcf554

Source message: Move inline TODO items to Github issue
2024-12-05 05:53:31 +00:00

679 lines
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YAML
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name: "pre_processing"
namespace: "workflows"
version: "add-labels"
argument_groups:
- name: "Inputs"
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"
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: false
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, reverse\
\ or auto"
info: null
default:
- "auto"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--bbsplit_index"
description: "BBsplit index"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--ribo_database_manifest"
description: "Text file containing paths to fasta files (one per line) that will\
\ be used to create the database for SortMeRNA."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--transcript_fasta"
description: "Path to FASTA transcriptome file."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--gtf"
description: "Path to GTF annotation file."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--salmon_index"
description: "Path to directory containing the Salmon index"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--num_trimmed_reads"
description: "Number of reads after trimming"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Extra pipeline options"
arguments:
- type: "boolean"
name: "--skip_qc"
description: "Skip QC steps of the workflow."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "FastQC options"
arguments:
- type: "boolean"
name: "--skip_fastqc"
description: "Skip FatQC step."
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "UMI-tools options"
arguments:
- 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_umi_extract"
description: "Skip umi_tools extract step."
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umitools_extract_method"
description: "UMI pattern to use."
info: null
default:
- "string"
required: false
choices:
- "string"
- "regex"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umitools_bc_pattern"
description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\
\ first 6 nucleotides of the read are from the UMI."
info: null
default:
- ""
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umitools_bc_pattern2"
description: "The UMI barcode pattern to use if the UMI is located in read 2."
info: null
default:
- ""
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--umi_discard_read"
description: "After UMI barcode extraction discard either R1 or R2 by setting\
\ this parameter to 1 or 2, respectively."
info: null
default:
- 0
required: false
choices:
- 0
- 1
- 2
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umitools_umi_separator"
description: "The character that separates the UMI in the read name. Most likely\
\ a colon if you skipped the extraction with UMI-tools and used other software."
info: null
default:
- "_"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umitools_grouping_method"
description: "Method to use to determine read groups by subsuming those with similar\
\ UMIs. All methods start by identifying the reads with the same mapping position,\
\ but treat similar yet nonidentical UMIs differently."
info: null
default:
- "directional"
required: false
choices:
- "unique"
- "percentile"
- "cluster"
- "adjacency"
- "directional"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--save_umi_intermeds"
description: "If this option is specified, intermediate FastQ and BAM files produced\
\ by UMI-tools are also saved in the results directory."
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Read trimming options"
arguments:
- type: "string"
name: "--trimmer"
description: "Specify the trimming tool to use."
info: null
default:
- "trimgalore"
required: false
choices:
- "trimgalore"
- "fastp"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--min_trimmed_reads"
description: "Minimum number of trimmed reads below which samples are removed\
\ from further processing. Some downstream steps in the pipeline will fail if\
\ this threshold is too low."
info: null
default:
- 10000
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--skip_trimming"
description: "Skip the adapter trimming step."
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--save_trimmed"
description: "Save the trimmed FastQ files in the results directory."
info: null
default:
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Read filtering options"
arguments:
- type: "boolean_true"
name: "--skip_bbsplit"
description: "Skip BBSplit for removal of non-reference genome reads."
info: null
direction: "input"
- type: "boolean_true"
name: "--remove_ribo_rna"
description: "Enable the removal of reads derived from ribosomal RNA using SortMeRNA."
info: null
direction: "input"
- name: "Output"
arguments:
- type: "file"
name: "--qc_output1"
description: "Path to output directory"
info: null
default:
- "${id}_r1.fastq.gz"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--qc_output2"
description: "Path to output directory"
info: null
default:
- "${id}_r2.fastq.gz"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastqc_html_1"
description: "FastQC HTML report for read 1."
info: null
default:
- "${id}_r1.fastqc.html"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastqc_html_2"
description: "FastQC HTML report for read 2."
info: null
default:
- "${id}_r2.fastqc.html"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastqc_zip_1"
description: "FastQC report archive for read 1."
info: null
default:
- "${id}_r1.fastqc.zip"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastqc_zip_2"
description: "FastQC report archive for read 2."
info: null
default:
- "${id}_r2.fastqc.zip"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_log_1"
info: null
default:
- "${id}_r1.trimming_report.txt"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_log_2"
info: null
default:
- "${id}_r2.trimming_report.txt"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_html_1"
info: null
default:
- "${id}_r1.trimmed_fastqc.html"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_html_2"
info: null
default:
- "${id}_r2.trimmed_fastqc.html"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_zip_1"
info: null
default:
- "${id}_r1.trimmed_fastqc.zip"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_zip_2"
info: null
default:
- "${id}_r2.trimmed_fastqc.zip"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--sortmerna_log"
description: "Sortmerna log file."
info: null
default:
- "$id.sortmerna.log"
must_exist: false
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--salmon_quant_output"
description: "Results from Salmon quant"
info: null
default:
- "$id.salmon_quant_output"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_json"
description: "The fastp json format report file name"
info: null
default:
- "$id.fastp_out.json"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--trim_html"
description: "The fastp html format report file name"
info: null
default:
- "$id.fastp_out.html"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--merged_out"
description: "File name to store merged fastp output."
info: null
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 subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline.\n"
info: null
status: "enabled"
requirements:
commands:
- "ps"
dependencies:
- name: "fastqc"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
- name: "umi_tools/umi_tools_extract"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
- name: "trimgalore"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
- name: "bbmap/bbmap_bbsplit"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
- name: "sortmerna"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
- name: "fastp"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
- name: "fq_subsample"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
- name: "salmon/salmon_quant"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
repositories:
- type: "vsh"
name: "biobox"
repo: "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:
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/pre_processing/config.vsh.yaml"
runner: "executable"
engine: "native"
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "e244fcf554ffba49eafd8534e96f52004dcc5dee"
git_remote: "https://x-access-token:ghs_oXfZ3s5ZxhhPYHO3WtccDldZ2L7ev52GtUDQ@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/trimgalore"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/sortmerna"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fastp"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fq_subsample"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
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: "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"
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