Mercurial > repos > kkonganti > hfp_nowayout
diff 0.5.0/cpipes @ 0:97cd2f532efe
planemo upload
author | kkonganti |
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date | Mon, 31 Mar 2025 14:50:40 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.5.0/cpipes Mon Mar 31 14:50:40 2025 -0400 @@ -0,0 +1,58 @@ +#!/usr/bin/env nextflow + +/* +---------------------------------------------------------------------------------------- + cfsan-dev/cpipes +---------------------------------------------------------------------------------------- + NAME : CPIPES + DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA. + GITLAB : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework + JIRA : https://xxxxxxxxxx/jira/projects/CPIPES/ + CONTRIBUTORS : Kranti Konganti +---------------------------------------------------------------------------------------- +*/ + +// Enable DSL 2 +nextflow.enable.dsl = 2 + +// Default routines for MAIN +include { pipelineBanner; stopNow; } from "${params.routines}" + +// Our banner for CPIPES +log.info pipelineBanner() + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + INCLUDE ALL WORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +switch ("${params.pipeline}") { + case "nowayout": + include { NOWAYOUT } from "${params.workflows}${params.fs}${params.pipeline}" + break + default: + stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline nowayout") +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN ALL WORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow { + // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE" + // INSIDE WORKFLOW + switch ("${params.pipeline}") { + case "nowayout": + NOWAYOUT() + break + } +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + THE END +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/