Build branch main with version main (d0c648f)
Build pipeline: vsh-ci-template-p9886
Source commit: d0c648fb7e
Source message: Delete src/bgzip directory (#64)
It was moved to toolbox
This commit is contained in:
464
target/executable/multiqc/.config.vsh.yaml
Normal file
464
target/executable/multiqc/.config.vsh.yaml
Normal file
@@ -0,0 +1,464 @@
|
||||
name: "multiqc"
|
||||
version: "main"
|
||||
argument_groups:
|
||||
- name: "Input"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
description: "File paths to be searched for analysis results to be included in\
|
||||
\ the report.\n"
|
||||
info: null
|
||||
example:
|
||||
- "data/results"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Ouput"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--output_report"
|
||||
description: "Filepath of the generated report.\n"
|
||||
info: null
|
||||
example:
|
||||
- "multiqc_report.html"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_data"
|
||||
description: "Output directory for parsed data files. If not provided, parsed\
|
||||
\ data will not be published.\n"
|
||||
info: null
|
||||
example:
|
||||
- "multiqc_data"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output_plots"
|
||||
description: "Output directory for generated plots. If not provided, plots will\
|
||||
\ not be published.\n"
|
||||
info: null
|
||||
example:
|
||||
- "multiqc_plots"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Modules and analyses to run"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--include_modules"
|
||||
description: "Use only these module"
|
||||
info: null
|
||||
example:
|
||||
- "fastqc,cutadapt"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "string"
|
||||
name: "--exclude_modules"
|
||||
description: "Do not use only these modules"
|
||||
info: null
|
||||
example:
|
||||
- "fastqc,cutadapt"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "string"
|
||||
name: "--ignore_analysis"
|
||||
info: null
|
||||
example:
|
||||
- "run_one/*,run_two/*"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "string"
|
||||
name: "--ignore_samples"
|
||||
info: null
|
||||
example:
|
||||
- "sample_1*,sample_3*"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: true
|
||||
multiple_sep: ","
|
||||
- type: "boolean_true"
|
||||
name: "--ignore_symlinks"
|
||||
description: "Ignore symlinked directories and files"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "Sample name handling"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--dirs"
|
||||
description: "Prepend directory to sample names to avoid clashing filenames"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "integer"
|
||||
name: "--dirs_depth"
|
||||
description: "Prepend n directories to sample names. Negative number to take from\
|
||||
\ start of path."
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--full_names"
|
||||
description: "Do not clean the sample names (leave as full file name)"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--fn_as_s_name"
|
||||
description: "Use the log filename as the sample name"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "file"
|
||||
name: "--replace_names"
|
||||
description: "TSV file to rename sample names during report generation"
|
||||
info: null
|
||||
example:
|
||||
- "replace_names.tsv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Report Customisation"
|
||||
arguments:
|
||||
- type: "string"
|
||||
name: "--title"
|
||||
description: "Report title. Printed as page header, used for filename if not otherwise\
|
||||
\ specified.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--comment"
|
||||
description: "Custom comment, will be printed at the top of the report.\n"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--template"
|
||||
description: "Report template to use.\n"
|
||||
info: null
|
||||
required: false
|
||||
choices:
|
||||
- "default"
|
||||
- "gathered"
|
||||
- "geo"
|
||||
- "highcharts"
|
||||
- "sections"
|
||||
- "simple"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--sample_names"
|
||||
description: "TSV file containing alternative sample names for renaming buttons\
|
||||
\ in the report.\n"
|
||||
info: null
|
||||
example:
|
||||
- "sample_names.tsv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--sample_filters"
|
||||
description: "TSV file containing show/hide patterns for the report\n"
|
||||
info: null
|
||||
example:
|
||||
- "sample_filters.tsv"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--custom_css_file"
|
||||
description: "Custom CSS file to add to the final report\n"
|
||||
info: null
|
||||
example:
|
||||
- "custom_style_sheet.css"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--profile_runtime"
|
||||
description: "Add analysis of how long MultiQC takes to run to the report\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- name: "MultiQC behaviour"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--verbose"
|
||||
description: "Increase output verbosity.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--quiet"
|
||||
description: "Only show log warnings\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--strict"
|
||||
description: "Don't catch exceptions, run additional code checks to help development.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--development"
|
||||
description: "Development mode. Do not compress and minimise JS, export uncompressed\
|
||||
\ plot data.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--require_logs"
|
||||
description: "Require all explicitly requested modules to have log files. If not,\
|
||||
\ MultiQC will exit with an error.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--no_megaqc_upload"
|
||||
description: "Don't upload generated report to MegaQC, even if MegaQC options\
|
||||
\ are found.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--no_ansi"
|
||||
description: "Disable coloured log output.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--cl_config"
|
||||
description: "YAML formatted string that allows to customize MultiQC behaviour\
|
||||
\ like input file detection.\n"
|
||||
info: null
|
||||
example:
|
||||
- "qualimap_config: { general_stats_coverage: [20,40,200] }"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- name: "Output format"
|
||||
arguments:
|
||||
- type: "boolean_true"
|
||||
name: "--flat"
|
||||
description: "Use only flat plots (static images).\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--interactive"
|
||||
description: "Use only interactive plots (in-browser Javascript).\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--data_dir"
|
||||
description: "Force the parsed data directory to be created.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--no_data_dir"
|
||||
description: "Prevent the parsed data directory from being created.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "boolean_true"
|
||||
name: "--zip_data_dir"
|
||||
description: "Compress the data directory.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
- type: "string"
|
||||
name: "--data_format"
|
||||
description: "Output parsed data in a different format than the default 'txt'.\n"
|
||||
info: null
|
||||
required: false
|
||||
choices:
|
||||
- "tsv"
|
||||
- "csv"
|
||||
- "json"
|
||||
- "yaml"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean_true"
|
||||
name: "--pdf"
|
||||
description: "Creates PDF report with the 'simple' template. Requires Pandoc to\
|
||||
\ be installed.\n"
|
||||
info: null
|
||||
direction: "input"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
is_executable: true
|
||||
description: "MultiQC aggregates results from bioinformatics analyses across many\
|
||||
\ samples into a single report.\nIt searches a given directory for analysis logs\
|
||||
\ and compiles a HTML report. It's a general use tool, perfect for summarising the\
|
||||
\ output from numerous bioinformatics tools.\n"
|
||||
test_resources:
|
||||
- type: "bash_script"
|
||||
path: "test.sh"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "test_data"
|
||||
info:
|
||||
keywords:
|
||||
- "QC"
|
||||
- "html report"
|
||||
- "aggregate analysis"
|
||||
links:
|
||||
homepage: "https://multiqc.info/"
|
||||
documentation: "https://multiqc.info/docs/"
|
||||
repository: "https://github.com/MultiQC/MultiQC"
|
||||
references:
|
||||
doi: "10.1093/bioinformatics/btw354"
|
||||
licence: "GPL v3 or later"
|
||||
status: "enabled"
|
||||
requirements:
|
||||
commands:
|
||||
- "ps"
|
||||
license: "MIT"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/biobox"
|
||||
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: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "main"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "multiqc --version | sed 's/multiqc, version\\s\\(.*\\)/multiqc: \"\\1\"/' >\
|
||||
\ /var/software_versions.txt\n"
|
||||
test_setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "jq"
|
||||
interactive: false
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/multiqc/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/multiqc"
|
||||
executable: "target/executable/multiqc/multiqc"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "d0c648fb7eefe067f5b5b3d402a204354bb37198"
|
||||
git_remote: "https://github.com/viash-hub/biobox"
|
||||
package_config:
|
||||
name: "biobox"
|
||||
version: "main"
|
||||
description: "A collection of bioinformatics tools for working with sequence data.\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC6"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".requirements.commands := ['ps']\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'main'"
|
||||
keywords:
|
||||
- "bioinformatics"
|
||||
- "modules"
|
||||
- "sequencing"
|
||||
license: "MIT"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/viash-hub/biobox"
|
||||
issue_tracker: "https://github.com/viash-hub/biobox/issues"
|
||||
1945
target/executable/multiqc/multiqc
Executable file
1945
target/executable/multiqc/multiqc
Executable file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user