From de76ce114b3f1770717b19a0c72432f4deb22581 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 25 Oct 2021 09:43:49 +0200
Subject: [PATCH] danpos: allow collect for fastq input to determine if data
 are paired-end

---
 src/nf_modules/danpos/main.nf | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index e78d35c5..a2d1a18e 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -59,6 +59,9 @@ process dpos_bam {
   if (fastq.size() == 2){
     m = 1
   }
+  if (fastq.size() > 2 & fastq[0].size() == 2){
+    m = 1
+  }
 """
 danpos.py dpos -m ${m} \
   ${params.dpos} \
@@ -119,6 +122,9 @@ process dpos_wig {
   if (fastq.size() == 2){
     m = 1
   }
+  if (fastq.size() > 2 & fastq[0].size() == 2){
+    m = 1
+  }
 """
 danpos.py dpos -m ${m} \
   ${params.dpos} \
@@ -184,6 +190,9 @@ process dpos_wigvswig {
   if (fastq.size() == 2){
     m = 1
   }
+  if (fastq.size() > 2 & fastq[0].size() == 2){
+    m = 1
+  }
 """
 danpos.py dpos -m ${m} \
   ${params.dpos} \
@@ -234,6 +243,9 @@ process dpeak_bam {
   if (fastq.size() == 2){
     m = 1
   }
+  if (fastq.size() > 2 & fastq[0].size() == 2){
+    m = 1
+  }
 """
 danpos.py dpeak -m ${m} \
   ${params.dpeak} \
@@ -296,6 +308,9 @@ process dpeak_wig {
   if (fastq.size() == 2){
     m = 1
   }
+  if (fastq.size() > 2 & fastq[0].size() == 2){
+    m = 1
+  }
 """
 danpos.py dpeak -m ${m} \
   ${params.dpeak} \
@@ -364,6 +379,9 @@ process dpeak_wigvswig {
   if (fastq.size() == 2){
     m = 1
   }
+  if (fastq.size() > 2 & fastq[0].size() == 2){
+    m = 1
+  }
 """
 danpos.py dpeak -m ${m} \
   ${params.dpeak} \
-- 
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