2022-02-18 06:55:14 +00:00
|
|
|
#!/usr/bin/env nextflow
|
|
|
|
/*
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
nf-core/taxprofiler
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
Github : https://github.com/nf-core/taxprofiler
|
2022-08-30 13:43:03 +00:00
|
|
|
Website: https://nf-co.re/taxprofiler
|
2022-02-18 06:55:14 +00:00
|
|
|
Slack : https://nfcore.slack.com/channels/taxprofiler
|
|
|
|
----------------------------------------------------------------------------------------
|
|
|
|
*/
|
|
|
|
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
|
|
|
|
/*
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
GENOME PARAMETER VALUES
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
*/
|
|
|
|
|
|
|
|
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
|
|
|
|
|
|
|
|
/*
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
VALIDATE & PRINT PARAMETER SUMMARY
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
*/
|
|
|
|
|
|
|
|
WorkflowMain.initialise(workflow, params, log)
|
|
|
|
|
|
|
|
/*
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
NAMED WORKFLOW FOR PIPELINE
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
*/
|
|
|
|
|
|
|
|
include { TAXPROFILER } from './workflows/taxprofiler'
|
|
|
|
|
|
|
|
//
|
|
|
|
// WORKFLOW: Run main nf-core/taxprofiler analysis pipeline
|
|
|
|
//
|
|
|
|
workflow NFCORE_TAXPROFILER {
|
|
|
|
TAXPROFILER ()
|
|
|
|
}
|
|
|
|
|
|
|
|
/*
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
RUN ALL WORKFLOWS
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
*/
|
|
|
|
|
|
|
|
//
|
|
|
|
// WORKFLOW: Execute a single named workflow for the pipeline
|
|
|
|
// See: https://github.com/nf-core/rnaseq/issues/619
|
|
|
|
//
|
|
|
|
workflow {
|
|
|
|
NFCORE_TAXPROFILER ()
|
|
|
|
}
|
|
|
|
|
|
|
|
/*
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
THE END
|
2022-03-15 21:05:37 +00:00
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
2022-02-18 06:55:14 +00:00
|
|
|
*/
|