Nextflow Registry | nf-core/bases2fastq@0.0.0-0c7146d

nf-core/bases2fastq @ 0.0.0-0c7146d

Demultiplex Element Biosciences bases files

demultiplex element fastq

Latest version: 0.0.0-0c7146d

Total downloads: 5

Source: nf-core/modules

Authors: @edmundmiller

Maintainers: @edmundmiller

Demultiplex Element Biosciences bases files

Add the following snippet to your workflow script to include this module.

include { BASES2FASTQ } from 'nf-core/bases2fastq'

MIT License

Process

`Name`	`BASES2FASTQ`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`run_manifest` file	RunManifest file `*.{csv}`
`run_dir` directory	Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied

Output 9 channels

#1 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/Metrics.csv` file	Sample metrics `${prefix}/Metrics.csv`

#2 qc_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*_QC.html` file	QC HTML report `${prefix}//*_QC.html`

#3 run_stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/RunStats.json` file	QC HTML report `${prefix}/*.html`

#4 unassigned tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/UnassignedSequences.csv` file	Unassigned Sequences `${prefix}/UnassignedSequences.csv`

#5 sample_json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/Samples/*/_stats.json` file	Demultiplexed sample stats `${prefix}/Samples//.json`

#6 sample_fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/Samples/*/_R*.fastq.gz` file	Demultiplexed sample FASTQ files `${prefix}/Samples//_R*.fastq.gz`

#7 multiqc_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/multiqc_report.html` file	Multiqc HTML report `${prefix}/multiqc_report.html`

#8 versions_bases2fastq tuple

`${task.process}` string	The process the versions were collected from
`bases2fastq` string	The tool name
`bases2fastq --version \| sed "s/.version //;s/,.//"` string	The command used to generate the version of the tool

#9 generated_run_manifest tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/RunManifest.json` file	Updated Run Manifest JSON from the run_manifest csv `${prefix}/RunManifest.json`

Tool	Description	Homepage
bases2fastq	Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis	https://go.elementbiosciences.com/bases2fastq-download