From 60224e9149b0212aa63d8af0785b71b8c2935224 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 8 Sep 2022 14:25:23 +0200
Subject: [PATCH] Patch fastp until I have an OK on the module update

---
 modules.json                             |  3 ++-
 modules/nf-core/modules/fastp/fastp.diff | 33 ++++++++++++++++++++++++
 modules/nf-core/modules/fastp/main.nf    |  7 ++---
 3 files changed, 39 insertions(+), 4 deletions(-)
 create mode 100644 modules/nf-core/modules/fastp/fastp.diff

diff --git a/modules.json b/modules.json
index 5a62e0c..3b8cab2 100644
--- a/modules.json
+++ b/modules.json
@@ -43,7 +43,8 @@
                 },
                 "fastp": {
                     "branch": "master",
-                    "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f"
+                    "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f",
+                    "patch": "modules/nf-core/modules/fastp/fastp.diff"
                 },
                 "fastqc": {
                     "branch": "master",
diff --git a/modules/nf-core/modules/fastp/fastp.diff b/modules/nf-core/modules/fastp/fastp.diff
new file mode 100644
index 0000000..a05d486
--- /dev/null
+++ b/modules/nf-core/modules/fastp/fastp.diff
@@ -0,0 +1,33 @@
+Changes in module 'nf-core/modules/fastp'
+--- modules/nf-core/modules/fastp/main.nf
++++ modules/nf-core/modules/fastp/main.nf
+@@ -33,9 +33,8 @@
+         def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
+         """
+         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
+-        cat ${prefix}.fastq.gz \\
+-        | fastp \\
+-            --stdin \\
++        
++        fastp \\
+             --stdout \\
+             --in1 ${prefix}.fastq.gz \\
+             --thread $task.cpus \\
+@@ -45,6 +44,7 @@
+             $args \\
+             2> ${prefix}.fastp.log \\
+         | gzip -c > ${prefix}.fastp.fastq.gz
++
+         cat <<-END_VERSIONS > versions.yml
+         "${task.process}":
+             fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+@@ -69,6 +69,7 @@
+             --detect_adapter_for_pe \\
+             $args \\
+             2> ${prefix}.fastp.log
++            
+ 
+         cat <<-END_VERSIONS > versions.yml
+         "${task.process}":
+
+************************************************************
diff --git a/modules/nf-core/modules/fastp/main.nf b/modules/nf-core/modules/fastp/main.nf
index d9134e1..abbdbad 100644
--- a/modules/nf-core/modules/fastp/main.nf
+++ b/modules/nf-core/modules/fastp/main.nf
@@ -33,9 +33,8 @@ process FASTP {
         def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
-        cat ${prefix}.fastq.gz \\
-        | fastp \\
-            --stdin \\
+        
+        fastp \\
             --stdout \\
             --in1 ${prefix}.fastq.gz \\
             --thread $task.cpus \\
@@ -45,6 +44,7 @@ process FASTP {
             $args \\
             2> ${prefix}.fastp.log \\
         | gzip -c > ${prefix}.fastp.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
@@ -69,6 +69,7 @@ process FASTP {
             --detect_adapter_for_pe \\
             $args \\
             2> ${prefix}.fastp.log
+            
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":