Nextflow Registry | nf-core/mgikit/demultiplex@0.0.0-6c4ed3a

nf-core/mgikit/demultiplex @ 0.0.0-6c4ed3a

Demultiplex MGI fastq files

demultiplex mgi fastq

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @ziadbkh

Demultiplex MGI fastq files

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

include { MGIKIT_DEMULTIPLEX } from 'nf-core/mgikit/demultiplex'

MIT License

Process

`Name`	`MGIKIT_DEMULTIPLEX`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`samplesheet` file	Input samplesheet `*.{csv}`
`run_dir` file	Input run directory containing BioInfo.csv and fastq data. fastq files should be in MGI format and can be either single or paired end.

Output 10 channels

#1 fastq tuple

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

#2 ambiguous tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}_ambiguous/*.fastq.gz` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `Ambiguous*.fastq.gz`

#3 qc_reports tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}/*mgikit.{info,general,ambiguous_barcode,undetermined_barcode}` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `mgikit.{info,general,ambiguous_barcode,undetermined_barcode}`

#4 undetermined tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}_undetermined/*.fastq.gz` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `Undetermined*.fastq.gz`

#5 index_reports tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}/*mgikit.info` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*mgikit.info`

#6 versions_mgikit tuple

`${task.process}` string	The process the versions were collected from
`mgikit` string	The tool name
`mgikit --version \| sed -n "s/.*kit. //p"` string	The command used to generate the version of the tool

#7 ambiguous_reports tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}/mgikit.ambiguous_barcode` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `mgikit.ambiguous_barcode`

#8 sample_stat_reports tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}/*mgikit.sample_stats` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*mgikit.sample_stats`

#9 general_info_reports tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}/*mgikit.general` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*mgikit.general`

#10 undetermined_reports tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*.fastq.gz`
`${prefix}/mgikit.undetermined_barcode` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ] `*mgikit.undetermined_barcode`