From b67459c774762112ae21f8438b6268825a4edf16 Mon Sep 17 00:00:00 2001
From: Tyler Chafin <tc25@sanger.ac.uk>
Date: Mon, 9 Sep 2024 16:02:26 +0100
Subject: [PATCH] spoof REF_PATH to disallow remote lookkup for cram

---
 conf/modules.config | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index a2d4464..44d6cf0 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -12,6 +12,7 @@
 
 process {
     withName: SAMTOOLS_FASTQ {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = '-F 0x200 -nt'
     }
 
@@ -24,6 +25,7 @@ process {
     }
 
     withName: SAMTOOLS_MERGE {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = { "-c -p" }
         ext.prefix = { "${meta.id}.merge" }
     }
@@ -35,6 +37,7 @@ process {
     }
 
     withName: SAMTOOLS_COLLATETOFASTA {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args   = { (params.use_work_dir_as_temp ? "-T." : "") }
     }
 
@@ -43,6 +46,7 @@ process {
     }
 
     withName: SAMTOOLS_CONVERT {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = "-be '[rq]>=0.99' -x fi -x fp -x ri -x rp --write-index"
     }
 
@@ -64,6 +68,7 @@ process {
     }
 
     withName: '.*:CONVERT_STATS:SAMTOOLS_CRAM' {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.prefix = { "${fasta.baseName}.${meta.datatype}.${meta.id}" }
         ext.args   = '--output-fmt cram --write-index'
     }
@@ -82,6 +87,7 @@ process {
     }
 
     withName: SAMTOOLS_STATS {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.prefix = { "${input.baseName}" }
     }
 
@@ -91,6 +97,7 @@ process {
     }
 
     withName: '.*:CONVERT_STATS:SAMTOOLS_.*' {
+        beforeScript = { "export REF_PATH=spoof"}
         publishDir = [
             path: { "${params.outdir}/read_mapping/${meta.datatype}" },
             mode: params.publish_dir_mode,