CI
6f2f840fd9
Build pipeline: viash-hub.biobox.main-zp6tq
Source commit: 7f8bcc2b3e
Source message: BD rhapsody sequence analysis (#96)
* wip
* fix test
* add help
* update 2.2 args
* fix bug
* extend test data
* output separate files
* analyse missing args
* tweaks to test
* fix script
* fix test
* fix test
* move small reference
* wip generate wta test data
* don't forget about umi in r1
* remove unneeded pkg
* load reference in memory just once
* fix random choices
* extend test
* add abc immunediscoverypanel
* wip abc testing code
* fix abc test; need unique instrument, run and flowcell ids for each sample
* add smk data
* add entry to changelog
* remove old test file
* adapt test for missing read
* update description
* add comment
* ensure cwl files are absolute
* Apply suggestions from code review
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* fix suggestion
* newer pipelines have docker requirements as a hint instead of a strict requirement
* rename str to content
* remove deleted resources
* fix containers
* fix script
* fix suggestion
* fix suggestion...
* fix test
* fix component name
* fix test
* apply suggestions
* fix test
* added note
* fix changelog
* fix changelog again
* splitting hairs here
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
484 lines
13 KiB
YAML
484 lines
13 KiB
YAML
name: "multiqc"
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version: "main"
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authors:
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- name: "Dorien Roosen"
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roles:
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- "author"
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- "maintainer"
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info:
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links:
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email: "dorien@data-intuitive.com"
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github: "dorien-er"
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linkedin: "dorien-roosen"
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organizations:
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- name: "Data Intuitive"
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href: "https://www.data-intuitive.com"
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role: "Data Scientist"
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argument_groups:
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- name: "Input"
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arguments:
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- type: "file"
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name: "--input"
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description: "File paths to be searched for analysis results to be included in\
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\ the report.\n"
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info: null
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example:
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- "data/results"
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- name: "Ouput"
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arguments:
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- type: "file"
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name: "--output_report"
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description: "Filepath of the generated report.\n"
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info: null
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example:
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- "multiqc_report.html"
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must_exist: false
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--output_data"
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description: "Output directory for parsed data files. If not provided, parsed\
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\ data will not be published.\n"
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info: null
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example:
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- "multiqc_data"
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must_exist: false
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--output_plots"
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description: "Output directory for generated plots. If not provided, plots will\
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\ not be published.\n"
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info: null
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example:
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- "multiqc_plots"
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must_exist: false
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create_parent: true
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required: false
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direction: "output"
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multiple: false
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multiple_sep: ";"
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- name: "Modules and analyses to run"
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arguments:
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- type: "string"
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name: "--include_modules"
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description: "Use only these module"
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info: null
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example:
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- "fastqc"
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- "cutadapt"
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required: false
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- type: "string"
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name: "--exclude_modules"
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description: "Do not use only these modules"
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info: null
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example:
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- "fastqc"
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- "cutadapt"
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required: false
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- type: "string"
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name: "--ignore_analysis"
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info: null
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example:
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- "run_one/*"
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- "run_two/*"
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required: false
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- type: "string"
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name: "--ignore_samples"
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info: null
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example:
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- "sample_1*"
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- "sample_3*"
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required: false
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direction: "input"
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multiple: true
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--ignore_symlinks"
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description: "Ignore symlinked directories and files"
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info: null
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direction: "input"
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- name: "Sample name handling"
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arguments:
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- type: "boolean_true"
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name: "--dirs"
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description: "Prepend directory to sample names to avoid clashing filenames"
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info: null
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direction: "input"
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- type: "integer"
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name: "--dirs_depth"
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description: "Prepend n directories to sample names. Negative number to take from\
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\ start of path."
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--full_names"
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description: "Do not clean the sample names (leave as full file name)"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--fn_as_s_name"
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description: "Use the log filename as the sample name"
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info: null
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direction: "input"
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- type: "file"
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name: "--replace_names"
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description: "TSV file to rename sample names during report generation"
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info: null
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example:
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- "replace_names.tsv"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Report Customisation"
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arguments:
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- type: "string"
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name: "--title"
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description: "Report title. Printed as page header, used for filename if not otherwise\
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\ specified.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--comment"
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description: "Custom comment, will be printed at the top of the report.\n"
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info: null
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "string"
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name: "--template"
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description: "Report template to use.\n"
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info: null
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required: false
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choices:
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- "default"
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- "gathered"
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- "geo"
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- "highcharts"
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- "sections"
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- "simple"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--sample_names"
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description: "TSV file containing alternative sample names for renaming buttons\
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\ in the report.\n"
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info: null
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example:
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- "sample_names.tsv"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--sample_filters"
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description: "TSV file containing show/hide patterns for the report\n"
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info: null
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example:
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- "sample_filters.tsv"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--custom_css_file"
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description: "Custom CSS file to add to the final report\n"
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info: null
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example:
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- "custom_style_sheet.css"
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must_exist: true
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create_parent: true
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--profile_runtime"
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description: "Add analysis of how long MultiQC takes to run to the report\n"
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info: null
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direction: "input"
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- name: "MultiQC behaviour"
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arguments:
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- type: "boolean_true"
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name: "--verbose"
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description: "Increase output verbosity.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--quiet"
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description: "Only show log warnings\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--strict"
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description: "Don't catch exceptions, run additional code checks to help development.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--development"
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description: "Development mode. Do not compress and minimise JS, export uncompressed\
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\ plot data.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--require_logs"
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description: "Require all explicitly requested modules to have log files. If not,\
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\ MultiQC will exit with an error.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--no_megaqc_upload"
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description: "Don't upload generated report to MegaQC, even if MegaQC options\
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\ are found.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--no_ansi"
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description: "Disable coloured log output.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--cl_config"
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description: "YAML formatted string that allows to customize MultiQC behaviour\
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\ like input file detection.\n"
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info: null
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example:
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- "qualimap_config: { general_stats_coverage: [20,40,200] }"
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required: false
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- name: "Output format"
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arguments:
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- type: "boolean_true"
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name: "--flat"
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description: "Use only flat plots (static images).\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--interactive"
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description: "Use only interactive plots (in-browser Javascript).\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--data_dir"
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description: "Force the parsed data directory to be created.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--no_data_dir"
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description: "Prevent the parsed data directory from being created.\n"
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info: null
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direction: "input"
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- type: "boolean_true"
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name: "--zip_data_dir"
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description: "Compress the data directory.\n"
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info: null
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direction: "input"
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- type: "string"
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name: "--data_format"
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description: "Output parsed data in a different format than the default 'txt'.\n"
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info: null
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required: false
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choices:
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- "tsv"
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- "csv"
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- "json"
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- "yaml"
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "boolean_true"
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name: "--pdf"
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description: "Creates PDF report with the 'simple' template. Requires Pandoc to\
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\ be installed.\n"
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info: null
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direction: "input"
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resources:
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- type: "bash_script"
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path: "script.sh"
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is_executable: true
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description: "MultiQC aggregates results from bioinformatics analyses across many\
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\ samples into a single report.\nIt searches a given directory for analysis logs\
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\ and compiles a HTML report. It's a general use tool, perfect for summarising the\
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\ output from numerous bioinformatics tools.\n"
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test_resources:
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- type: "bash_script"
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path: "test.sh"
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is_executable: true
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- type: "file"
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path: "test_data"
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info:
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keywords:
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- "QC"
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- "html report"
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- "aggregate analysis"
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links:
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homepage: "https://multiqc.info/"
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documentation: "https://multiqc.info/docs/"
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repository: "https://github.com/MultiQC/MultiQC"
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references:
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doi: "10.1093/bioinformatics/btw354"
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licence: "GPL v3 or later"
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status: "enabled"
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requirements:
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commands:
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- "ps"
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license: "MIT"
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links:
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repository: "https://github.com/viash-hub/biobox"
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runners:
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- type: "executable"
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id: "executable"
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docker_setup_strategy: "ifneedbepullelsecachedbuild"
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- type: "nextflow"
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id: "nextflow"
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directives:
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tag: "$id"
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auto:
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simplifyInput: true
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simplifyOutput: false
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transcript: false
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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debug: false
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container: "docker"
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engines:
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- type: "docker"
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id: "docker"
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image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
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target_registry: "images.viash-hub.com"
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target_tag: "main"
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namespace_separator: "/"
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setup:
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- type: "docker"
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run:
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- "multiqc --version | sed 's/multiqc, version\\s\\(.*\\)/multiqc: \"\\1\"/' >\
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\ /var/software_versions.txt\n"
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test_setup:
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- type: "apt"
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packages:
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- "jq"
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interactive: false
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/multiqc/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/multiqc"
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executable: "target/executable/multiqc/multiqc"
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viash_version: "0.9.0"
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git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
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git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
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git_tag: "v0.2.0-3-g7f8bcc2"
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package_config:
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name: "biobox"
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version: "main"
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description: "A collection of bioinformatics tools for working with sequence data.\n"
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info: null
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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- ".requirements.commands := ['ps']\n"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'main'"
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keywords:
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- "bioinformatics"
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- "modules"
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- "sequencing"
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license: "MIT"
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organization: "vsh"
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links:
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repository: "https://github.com/viash-hub/biobox"
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issue_tracker: "https://github.com/viash-hub/biobox/issues"
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