From bc804b31331b30ac56f4d6277a2670f7b7f29185 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 25 Oct 2021 09:55:26 +0200
Subject: [PATCH] danpos: change the way to compute fastq size

---
 src/nf_modules/danpos/main.nf | 42 ++++++++++-------------------------
 1 file changed, 12 insertions(+), 30 deletions(-)

diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index a2d1a18e..3b83fa6d 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -34,7 +34,7 @@ process dpos_bam {
   }
 
   input:
-    tuple val(fastq_id), path(fastq)
+    tuple val(fastq)
     tuple val(file_id), path(bam_ip), path(bam_wce)
 
   output:
@@ -56,10 +56,7 @@ process dpos_bam {
   }
 
   m = 0
-  if (fastq.size() == 2){
-    m = 1
-  }
-  if (fastq.size() > 2 & fastq[0].size() == 2){
+  if (fastq[1].size() == 2){
     m = 1
   }
 """
@@ -97,7 +94,7 @@ process dpos_wig {
   }
 
   input:
-    tuple val(fastq_id), path(fastq)
+    tuple val(fastq)
     tuple val(file_id), path(wig_ip)
 
   output:
@@ -119,10 +116,7 @@ process dpos_wig {
   }
 
   m = 0
-  if (fastq.size() == 2){
-    m = 1
-  }
-  if (fastq.size() > 2 & fastq[0].size() == 2){
+  if (fastq[1].size() == 2){
     m = 1
   }
 """
@@ -164,7 +158,7 @@ process dpos_wigvswig {
   }
 
   input:
-    tuple val(fastq_id), path(fastq)
+    tuple val(fastq)
     tuple val(file_id_a), path(wig_ip_a)
     tuple val(file_id_b), path(wig_ip_b)
 
@@ -187,10 +181,7 @@ process dpos_wigvswig {
   }
 
   m = 0
-  if (fastq.size() == 2){
-    m = 1
-  }
-  if (fastq.size() > 2 & fastq[0].size() == 2){
+  if (fastq[1].size() == 2){
     m = 1
   }
 """
@@ -217,7 +208,7 @@ process dpeak_bam {
   }
 
   input:
-    tuple val(fastq_id), path(fastq)
+    tuple val(fastq)
     tuple val(file_id), path(bam_ip), path(bam_wce)
 
   output:
@@ -240,10 +231,7 @@ process dpeak_bam {
   }
 
   m = 0
-  if (fastq.size() == 2){
-    m = 1
-  }
-  if (fastq.size() > 2 & fastq[0].size() == 2){
+  if (fastq[1].size() == 2){
     m = 1
   }
 """
@@ -283,7 +271,7 @@ process dpeak_wig {
   }
 
   input:
-    tuple val(fastq_id), path(fastq)
+    tuple val(fastq)
     tuple val(file_id), path(wig_ip), path(wig_wce)
 
   output:
@@ -305,10 +293,7 @@ process dpeak_wig {
   }
 
   m = 0
-  if (fastq.size() == 2){
-    m = 1
-  }
-  if (fastq.size() > 2 & fastq[0].size() == 2){
+  if (fastq[1].size() == 2){
     m = 1
   }
 """
@@ -353,7 +338,7 @@ process dpeak_wigvswig {
   }
 
   input:
-    tuple val(fastq_id), path(fastq)
+    tuple val(fastq)
     tuple val(file_id_a), path(wig_ip_a), path(wig_wce_a)
     tuple val(file_id_b), path(wig_ip_b), path(wig_wce_b)
 
@@ -376,10 +361,7 @@ process dpeak_wigvswig {
   }
 
   m = 0
-  if (fastq.size() == 2){
-    m = 1
-  }
-  if (fastq.size() > 2 & fastq[0].size() == 2){
+  if (fastq[1].size() == 2){
     m = 1
   }
 """
-- 
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