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main.nf
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#!/usr/bin/env nextflow
/*
#######################################
...._
..-``` ``.._
_--`` .-`````)
.-````----.....___../` /`` ```)
_.(-----._ -.,. _._ <_) ........ .-````)
(__ (_> (_/\_) ` .-`` `-._ -``)_
.-( .--````` .-----------. --. -. -._ .-`` )
/`--- /` /```` /.. /.vv.\...-.\ \ \ \ -```)
/`-- / |`)vV` `Vv| ). \ |____/ ---)
(__ / \| /````````| /.\ \ __.-` //// /`/````)
( / / v/ /``.....V\\ \/\ \ \ //// / _.)
( `-.. / /__ | .| / / \\\ /\ /// _.-
(_.-----/____ /`\___\ \ | | || | / _.-``
( _.r-\\ `//\ `\ \ \ \ // | \ ,.-’`
(__.-\ \ \ \\ ////| \_ \ ` \____/ / \\ /
`\. /// |\ \ `\. __ / /\\ |
`*-.________ | | \ \ _ / .^./ \\ |
! / / `-. \___/ .-./ | \\|
|| / ^._..., ( ) \|
||/ \. | \._./ v
(|) `-..’ ./
V ``...`
___
|_| | __
| |igh |hroughput
__ _ __ __ ___
|_| /_\ | |_| | | | __
|_|acterial / \ntimicrobia|__ | \estistance ann|__|tation of |__|enomes
#######################################
*/
/*
========================================================================================
edwardbirdlab/BALROG-MON
========================================================================================
Bacterial Antimicroal Resistance Annoation Pipeline.
#### Find information at:
https://github.com/edwardbirdlab/BALROG-MON
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl=2
if (params.workflow_opt == 'shortread_meta') {
ch_fastq = Channel.fromPath(params.sample_sheet) \
| splitCsv(header:true) \
| map { row-> tuple(row.sample, file(row.r1), file(row.r2)) }
ch_hostgen = Channel.fromPath(params.sample_sheet) \
| splitCsv(header:true) \
| map { row-> tuple(row.sample, file(row.refernce_genome)) }
}
if (params.workflow_opt == 'sr_qc_only') {
ch_fastq = Channel.fromPath(params.sample_sheet) \
| splitCsv(header:true) \
| map { row-> tuple(row.sample, file(row.r1), file(row.r2)) }
}
include { SHORT_READ_METAGENOMIC as SHORT_READ_METAGENOMIC } from './workflows/SHORT_READ_METAGENOMIC.nf'
include { SR_QC_ONLY as SR_QC_ONLY } from './workflows/SR_QC_ONLY.nf'
include { SR_MULTIQC as SR_MULTIQC } from './workflows/SR_MULTIQC.nf'
workflow {
if (params.workflow_opt == 'shortread_meta') {
SHORT_READ_METAGENOMIC(ch_fastq, ch_hostgen)
}
if (params.workflow_opt == 'sr_qc_only') {
SR_QC_ONLY(ch_fastq)
}
if (params.workflow_opt == 'sr_multiqc') {
SR_MULTIQC()
}
}