From d482fc3483546c6fa908e8d85e360b27672e3cd9 Mon Sep 17 00:00:00 2001
From: Kaur Alasoo <kauralasoo@gmail.com>
Date: Thu, 12 May 2022 12:21:07 +0300
Subject: [PATCH] Move include statements out of workflow definition

---
 main.nf | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/main.nf b/main.nf
index bacda5f..6594290 100644
--- a/main.nf
+++ b/main.nf
@@ -104,49 +104,49 @@ def run_info_message() {
   log.info "========================================="
 }
 
+include {align_reads} from './workflows/align_wf'
+include {count_features} from './workflows/featureCounts_wf'
+include {quant_exons} from './workflows/exonQuant_wf'
+include {quant_tx} from './workflows/txQuant_wf'
+include {quant_txrev} from './workflows/txrevQuant_wf'
+include {quant_leafcutter} from './workflows/leafcutter_wf'
+include { createBigWig } from './modules/utils'
+include { generate_mbv } from './workflows/mbv_wf'
+include { sample_correlation } from './modules/utils'
+
 workflow {
     run_info_message()
-
-    include {align_reads} from './workflows/align_wf'
     align_reads()
     
     if (params.run_ge_quant){
-        include {count_features} from './workflows/featureCounts_wf'
         count_features(align_reads.out.bam_sorted_by_name)
     }
 
     if (params.run_exon_quant) {
-        include {quant_exons} from './workflows/exonQuant_wf'
         quant_exons(align_reads.out.bam_sorted_by_name)
     }
 
     if (params.run_salmon) {
-        include {quant_tx} from './workflows/txQuant_wf'
         quant_tx(align_reads.out.trimmed_reads)
     }
 
     if (params.run_txrevise) {
-        include {quant_txrev} from './workflows/txrevQuant_wf'
         quant_txrev(align_reads.out.trimmed_reads)
     }
 
     if (params.run_leafcutter) {
-        include {quant_leafcutter} from './workflows/leafcutter_wf'
         quant_leafcutter(align_reads.out.bam_sorted_indexed)
     }
 
     if (params.generate_bigwig) {
-        include { createBigWig } from './modules/utils'
         createBigWig(align_reads.out.bam_sorted_indexed)
     }
 
     if (params.run_mbv){
-        include { generate_mbv } from './workflows/mbv_wf'
         generate_mbv(align_reads.out.bam_sorted_indexed)
     }
 
     if (params.run_sample_corr && params.run_ge_quant) { 
-        include { sample_correlation } from './modules/utils'
         sample_correlation(count_features.out.gene_feature_counts.collect(),
                             Channel.fromPath("$baseDir/assets/mdsplot_header.txt"),
                             Channel.fromPath("$baseDir/assets/heatmap_header.txt"))