From 73cbad2edede1642d260b1203bde3041dcd97c08 Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Mon, 23 Jun 2025 02:40:37 +0000
Subject: [PATCH 1/2] Sanitize restriction site tag to handle special
 characters

---
 modules/local/hicpro/get_restriction_fragments.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index 9d10014..f89d082 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/modules/local/hicpro/get_restriction_fragments.nf
@@ -1,5 +1,5 @@
 process GET_RESTRICTION_FRAGMENTS {
-    tag "$res_site"
+    tag "${res_site.replaceAll(/[^a-zA-Z0-9_-]/, '_')}"
     label 'process_low'
 
     conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3"

From 50ab2fd9c555e249af176901e5c5011b0c71ebdd Mon Sep 17 00:00:00 2001
From: Cursor Agent <cursoragent@cursor.com>
Date: Mon, 23 Jun 2025 02:49:43 +0000
Subject: [PATCH 2/2] Fix process tag formatting to handle special characters
 in filenames

---
 modules/local/hicpro/dnase_mapping_stats.nf  | 2 +-
 modules/nf-core/bowtie2/build/main.nf        | 2 +-
 modules/nf-core/bwa/index/main.nf            | 2 +-
 modules/nf-core/cooler/makebins/main.nf      | 2 +-
 modules/nf-core/custom/getchromsizes/main.nf | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index 8e85113..9abbe61 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/modules/local/hicpro/dnase_mapping_stats.nf
@@ -1,5 +1,5 @@
 process MAPPING_STATS_DNASE {
-    tag "$sample = $bam"
+    tag "${(meta.id + '_' + bam.baseName).replaceAll(/[^a-zA-Z0-9_-]/, '_')}"
     label 'process_medium'
 
     conda "bioconda::samtools=1.15.1"
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
index 9e2e0e5..5800758 100644
--- a/modules/nf-core/bowtie2/build/main.nf
+++ b/modules/nf-core/bowtie2/build/main.nf
@@ -1,5 +1,5 @@
 process BOWTIE2_BUILD {
-    tag "$fasta"
+    tag "${fasta.baseName.replaceAll(/[^a-zA-Z0-9_-]/, '_')}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf
index 24b5a2e..d9912de 100644
--- a/modules/nf-core/bwa/index/main.nf
+++ b/modules/nf-core/bwa/index/main.nf
@@ -1,5 +1,5 @@
 process BWA_INDEX {
-    tag "$fasta"
+    tag "${fasta.baseName.replaceAll(/[^a-zA-Z0-9_-]/, '_')}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
diff --git a/modules/nf-core/cooler/makebins/main.nf b/modules/nf-core/cooler/makebins/main.nf
index 8a41556..99adb57 100644
--- a/modules/nf-core/cooler/makebins/main.nf
+++ b/modules/nf-core/cooler/makebins/main.nf
@@ -1,5 +1,5 @@
 process COOLER_MAKEBINS {
-    tag "${meta.id}}"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
index e8084ea..5b2cfa4 100644
--- a/modules/nf-core/custom/getchromsizes/main.nf
+++ b/modules/nf-core/custom/getchromsizes/main.nf
@@ -1,5 +1,5 @@
 process CUSTOM_GETCHROMSIZES {
-    tag "$fasta"
+    tag "${fasta.baseName.replaceAll(/[^a-zA-Z0-9_-]/, '_')}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"