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viash config
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dorien-er committed Feb 13, 2024
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194 changes: 194 additions & 0 deletions src/multiqc/config.vsh.yaml
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functionality:
name: "multiqc"
description: |
MultiQC aggregates results from bioinformatics analyses across many samples into a single report.
It 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.
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

argument_groups:
- name: "Input"
arguments:
- name: "--input"
type: file
multiple: true
example: data/,data/*_sample.zip,/tmp/results
description: |
File paths to be searched for analysis results to be included in the report.
- name: "--input_file"
type: file
example: path/to/input_file.txt
description: |
Supply a file containing a list of file paths to be searched, one per row
- name: "--multiqc_custom_config"
type: file
example: path/to/multiqc_config.yml
description: |
Specific config file to load, after those in MultiQC dir / home dir / working dir
- name: "Modules and analyses to run"
arguments:
- name: "--include_modules"
type: string
multiple: true
example: fastqc,cutadapt
description: Use only these module
- name: "--exclude_modules"
type: string
multiple: true
example: fastqc,cutadapt
description: Do not use only these modules
- name: "--ignore_analysis"
type: string
multiple: true
example: run_one/*,run_two/*
- name: "--ignore_samples"
type: string
multiple: true
example: sample_1*,sample_3*
- name: "--ignore_symlinks"
type: boolean_true
description: Ignore symlinked directories and files

- name: "Sample name handling"
arguments:
- name: "--dirs"
type: boolean_true
description: Prepend directory to sample names to avoid clashing filenames
- name: "--dirs_depth"
type: integer
description: Prepend n directories to sample names. Negative number to take from start of path.
- name: "--full_names"
type: boolean_true
description: Do not clean the sample names (leave as full file name)
- name: "--fn_as_s_name"
type: boolean_true
description: Use the log filename as the sample name
- name: "--replace_names"
type: file
example: replace_names.tsv
description: TSV file to rename sample names during report generation

- name: "Report Customisation"
arguments:
- name: "--title"
type: string
description: Report title. Printed as page header, used for filename if not otherwise specified.
- name: "--comment"
type: string
description: Custom comment, will be printed at the top of the report.
- name: "--template"
type: string
choices: [default, gathered, geo, highcharts, sections, simple]
description: Report template to use.
- name: "--sample_names"
type: file
description: TSV file containing alternative sample names for renaming buttons in the report.
example: sample_names.tsv
- name: "--sample_filters"
type: file
description: TSV file containing show/hide patterns for the report
example: sample_filters.tsv
- name: "--custom_css_file"
type: file
description: Custom CSS file to add to the final report
example: custom_style_sheet.css

- name: "MultiQC behaviour"
arguments:
- name: "--verbose"
type: boolean_true
description: Increase output verbosity.
- name: "--force"
type: boolean_true
description: Overwrite any existing reports
- name: "--quiet"
type: boolean_true
description: Only show log warnings
- name: "--strict"
type: boolean_true
description: Don't catch exceptions, run additional code checks to help development.
- name: "--development"
type: boolean_true
description: Development mode. Do not compress and minimise JS, export uncompressed plot data.
- name: "--require_logs"
type: boolean_true
description: Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.
- name: "--no_megaqc_upload"
type: boolean_true
description: Don't upload generated report to MegaQC, even if MegaQC options are found.
- name: "--no_ansi"
type: boolean_true
description: Disable coloured log output.

- name: "Ouput"
arguments:
- name: "--output"
type: file
direction: output
default: path/to/multiqc_report.html
- name: "--data"
type: file
direction: output
default: multiqc_data
- name: "--plots"
type: file
direction: output
default: multiqc_plots

- name: "Output format"
arguments:
- name: "--flat"
type: boolean_true
description: Use only flat plots (static images).
- name: "--interactive"
type: boolean_true
description: Use only interactive plots (in-browser Javascript).
- name: "--export"
type: boolean_true
description: Export plots as static images in addition to the report.
- name: "--data_dir"
type: boolean_true
description: Force the parsed data directory to be created.
- name: "--no_data_dir"
type: boolean_true
description: Prevent the parsed data directory from being created.
- name: "--zip_data_dir"
type: boolean_true
description: Compress the data directory.
- name: "--data_format"
type: string
choices: [tsv, csv, json, yaml]
description: Output parsed data in a different format.
- name: "--no_report"
type: boolean_true
description: Do not generate a report, only export data and plots.
- name: "--pdf"
type: boolean_true
description: Creates PDF report with the 'simple' template. Requires Pandoc to be installed.

resources:
- type: bash_script
path: script.sh

test_resources:
- type: bash_script
path: test.sh
- type: file
path: test_data

platforms:
- type: docker
image: quay.io/biocontainers/multiqc:1.20--pyhdfd78af_0
setup:
- type: docker
run: |
multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt
- type: nextflow

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