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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 | ||
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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 | ||
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- 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 | ||
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- 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 | ||
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- 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. | ||
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- 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 | ||
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- 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. | ||
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resources: | ||
- type: bash_script | ||
path: script.sh | ||
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test_resources: | ||
- type: bash_script | ||
path: test.sh | ||
- type: file | ||
path: test_data | ||
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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 |