Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.2/cpipes @ 108:2bda095a1222

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:24:42 -0400
parents 52045ea4679d
children
rev   line source
kkonganti@105 1 #!/usr/bin/env nextflow
kkonganti@105 2
kkonganti@105 3 /*
kkonganti@105 4 ----------------------------------------------------------------------------------------
kkonganti@105 5 cfsan-dev/cpipes
kkonganti@105 6 ----------------------------------------------------------------------------------------
kkonganti@105 7 NAME : CPIPES
kkonganti@105 8 DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@105 9 GITLAB : https://cfsan-git.fda.gov/cfsan-dev/cpipes
kkonganti@105 10 JIRA : https://sde.fda.gov/jira/projects/CPIPES/
kkonganti@105 11 CONTRIBUTORS : Kranti.Konganti@fda.hhs.gov
kkonganti@105 12 ----------------------------------------------------------------------------------------
kkonganti@105 13 */
kkonganti@105 14
kkonganti@105 15 // Enable DSL 2
kkonganti@105 16 nextflow.enable.dsl = 2
kkonganti@105 17
kkonganti@105 18 // Default routines for MAIN
kkonganti@105 19 include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@105 20
kkonganti@105 21 // Our banner for CPIPES
kkonganti@105 22 log.info pipelineBanner()
kkonganti@105 23
kkonganti@105 24 /*
kkonganti@105 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@105 26 NAMED WORKFLOW CAN BE USED TO RUN A SPECIFIC PIPELINE. THIS IS THE RECOMMENDED WAY.
kkonganti@105 27 NEED TO FIND A BETTER SOLUTION IF WE SEE A LOT OF PIPELINES.
kkonganti@105 28 See: https://github.com/nf-core/rnaseq/issues/619
kkonganti@105 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@105 30 */
kkonganti@105 31
kkonganti@105 32 switch ("${params.pipeline}") {
kkonganti@105 33 case "nanofactory":
kkonganti@105 34 include { NANOFACTORY } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@105 35 break
kkonganti@105 36 case "centriflaken":
kkonganti@105 37 include { CENTRIFLAKEN } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@105 38 break
kkonganti@105 39 case "centriflaken_hy":
kkonganti@105 40 include { CENTRIFLAKEN_HY } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@105 41 break
kkonganti@105 42 default:
kkonganti@105 43 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline centriflaken")
kkonganti@105 44 }
kkonganti@105 45
kkonganti@105 46 /*
kkonganti@105 47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@105 48 RUN ALL WORKFLOWS
kkonganti@105 49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@105 50 */
kkonganti@105 51
kkonganti@105 52 workflow {
kkonganti@105 53 // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE"
kkonganti@105 54 // INSIDE WORKFLOW
kkonganti@105 55 switch ("${params.pipeline}") {
kkonganti@105 56 case "nanofactory":
kkonganti@105 57 NANOFACTORY()
kkonganti@105 58 break
kkonganti@105 59 case "centriflaken":
kkonganti@105 60 CENTRIFLAKEN()
kkonganti@105 61 break
kkonganti@105 62 case "centriflaken_hy":
kkonganti@105 63 CENTRIFLAKEN_HY()
kkonganti@105 64 break
kkonganti@105 65 }
kkonganti@105 66 }
kkonganti@105 67
kkonganti@105 68 /*
kkonganti@105 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@105 70 THE END
kkonganti@105 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@105 72 */