4.13. bams_multiqc¶

Run FastQC on a set of BAM files, and then MultiQC to summarize all outputs.

4.13.1. Inputs¶

bams_multiqc.read_bams
Array[File]+ — Default: None
???

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bams_multiqc.fastqc.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

bams_multiqc.MultiQC.comment
String? — Default: None
???

bams_multiqc.MultiQC.config
File? — Default: None
???

bams_multiqc.MultiQC.config_yaml
String? — Default: None
???

bams_multiqc.MultiQC.data_dir
Boolean — Default: false
???

bams_multiqc.MultiQC.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

bams_multiqc.MultiQC.exclude_modules
Array[String]? — Default: None
???

bams_multiqc.MultiQC.export
Boolean — Default: false
???

bams_multiqc.MultiQC.file_name
String? — Default: None
???

bams_multiqc.MultiQC.flat
Boolean — Default: false
???

bams_multiqc.MultiQC.force
Boolean — Default: false
???

bams_multiqc.MultiQC.full_names
Boolean — Default: false
???

bams_multiqc.MultiQC.ignore_analysis_files
String? — Default: None
???

bams_multiqc.MultiQC.ignore_sample_names
String? — Default: None
???

bams_multiqc.MultiQC.interactive
Boolean — Default: true
???

bams_multiqc.MultiQC.lint
Boolean — Default: false
???

bams_multiqc.MultiQC.megaQC_upload
Boolean — Default: false
???

bams_multiqc.MultiQC.module_to_use
Array[String]? — Default: None
???

bams_multiqc.MultiQC.no_data_dir
Boolean — Default: false
???

bams_multiqc.MultiQC.out_dir
String — Default: "./multiqc-output"
???

bams_multiqc.MultiQC.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

bams_multiqc.MultiQC.pdf
Boolean — Default: false
???

bams_multiqc.MultiQC.sample_names
File? — Default: None
???

bams_multiqc.MultiQC.tag
String? — Default: None
???

bams_multiqc.MultiQC.template
String? — Default: None
???

bams_multiqc.MultiQC.title
String? — Default: None
???

bams_multiqc.MultiQC.zip_data_dir
Boolean — Default: false
???

bams_multiqc.fastqcs
Array[File]
???

bams_multiqc.multiqc
File
???

bams_multiqc.viral_core_version
String
???

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