From 30af2097d27ebad532dbc1264d5e607f70596ef0 Mon Sep 17 00:00:00 2001
From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:06:18 +0200
Subject: [PATCH 1/4] fix hisast2 index bug in yml file

---
 modules/local/ciriquant/yml/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf
index 4eb2d06f..42de10dc 100644
--- a/modules/local/ciriquant/yml/main.nf
+++ b/modules/local/ciriquant/yml/main.nf
@@ -19,7 +19,7 @@ process CIRIQUANT_YML {
     task.ext.when == null || task.ext.when
 
     script:
-    hisat2_prefix = meta2.id
+    hisat2_prefix = fasta.toString() - ~/.(fa|fasta)$/
     fasta_path = fasta.toRealPath()
     gtf_path = gtf.toRealPath()
     bwa_path = bwa.toRealPath()

From a860bf8d8e96a63443d9314fade2524cf6c2af8a Mon Sep 17 00:00:00 2001
From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:07:01 +0200
Subject: [PATCH 2/4] fix bug to make dir

---
 modules/local/ciriquant/ciriquant/main.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf
index 3ad0c34a..31d80e3a 100644
--- a/modules/local/ciriquant/ciriquant/main.nf
+++ b/modules/local/ciriquant/ciriquant/main.nf
@@ -24,6 +24,9 @@ process CIRIQUANT {
     prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '2.1.0'
     """
+    mkdir -p ${prefix}
+    mkdir -p ${prefix}/circ
+    touch ${prefix}/circ/${prefix}.ciri
     CIRIquant \\
         -t ${task.cpus} \\
         -1 ${reads[0]} \\

From 63cfd78d1ca4c1d61cb81aaafaefecc3662f1aed Mon Sep 17 00:00:00 2001
From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com>
Date: Thu, 11 Apr 2024 15:55:51 +0200
Subject: [PATCH 3/4] cleaner way to set hisat2_prefix

---
 modules/local/ciriquant/yml/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf
index 42de10dc..89c7048f 100644
--- a/modules/local/ciriquant/yml/main.nf
+++ b/modules/local/ciriquant/yml/main.nf
@@ -19,7 +19,7 @@ process CIRIQUANT_YML {
     task.ext.when == null || task.ext.when
 
     script:
-    hisat2_prefix = fasta.toString() - ~/.(fa|fasta)$/
+    hisat2_prefix = fasta.baseName
     fasta_path = fasta.toRealPath()
     gtf_path = gtf.toRealPath()
     bwa_path = bwa.toRealPath()

From cf0a05519a95a40994d6037644e2ef87c6cf4d31 Mon Sep 17 00:00:00 2001
From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com>
Date: Thu, 11 Apr 2024 16:03:41 +0200
Subject: [PATCH 4/4] revert back changes for testing

---
 modules/local/ciriquant/ciriquant/main.nf | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf
index 31d80e3a..3ad0c34a 100644
--- a/modules/local/ciriquant/ciriquant/main.nf
+++ b/modules/local/ciriquant/ciriquant/main.nf
@@ -24,9 +24,6 @@ process CIRIQUANT {
     prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = '2.1.0'
     """
-    mkdir -p ${prefix}
-    mkdir -p ${prefix}/circ
-    touch ${prefix}/circ/${prefix}.ciri
     CIRIquant \\
         -t ${task.cpus} \\
         -1 ${reads[0]} \\