Mercurial > repos > kkonganti > cfsan_cronology
diff 0.2.0/cpipes @ 11:a5f31c44f8c9
planemo upload
author | kkonganti |
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date | Mon, 15 Jul 2024 16:11:44 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.2.0/cpipes Mon Jul 15 16:11:44 2024 -0400 @@ -0,0 +1,56 @@ +#!/usr/bin/env nextflow + +/* +---------------------------------------------------------------------------------------- + cfsan/cpipes +---------------------------------------------------------------------------------------- + NAME : CPIPES + DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA. + GITLAB : https://xxxxxxxxx.fda.gov/Kranti.Konganti/cpipes-framework + JIRA : https://xxxxxxxxx.fda.gov/jira/projects/CPIPES/ + CONTRIBUTORS : Kranti.Konganti@fda.hhs.gov +---------------------------------------------------------------------------------------- +*/ + +// Enable DSL 2 +nextflow.enable.dsl = 2 + +// Default routines for MAIN +include { pipelineBanner; stopNow; } from "${params.routines}" + +// Our banner for CPIPES +log.info pipelineBanner() + +switch ("${params.pipeline}") { + case "cronology": + include { CRONOLOGY } from "${params.workflows}${params.fs}${params.pipeline}" + break + case "cronology_db": + include { CRONOLOGY_DB } from "${params.workflows}${params.fs}${params.pipeline}" + break + default: + stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline cronology") +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN ALL WORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow { + switch ("${params.pipeline}") { + case "cronology": + CRONOLOGY() + break + case "cronology_db": + CRONOLOGY_DB() + break + } +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + THE END +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/