From d5e47faa52d6a9f113348863f4ee76ea6235799b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Nov 2019 17:33:56 +0100
Subject: [PATCH] training_dataset.config: update conda_psmn.sh path to use
 $workflow

---
 src/training_dataset.config | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/training_dataset.config b/src/training_dataset.config
index 0220fab6..43e8588a 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -118,7 +118,7 @@ profiles {
   psmn {
     process{
       withName: build_synthetic_bed {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -128,7 +128,7 @@ profiles {
         queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
       }
       withName: fasta_from_bed {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -138,7 +138,7 @@ profiles {
         queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
       }
       withName: index_fasta {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -149,7 +149,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: mapping_fastq_paired {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -160,7 +160,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: bam_2_fastq_paired {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -171,7 +171,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_paired {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -182,7 +182,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_paired {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -193,7 +193,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: mapping_fastq_single {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -204,7 +204,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: bam_2_fastq_single {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -215,7 +215,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_single {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -226,7 +226,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_single {
-        beforeScript = "./src/conda_psmn.sh"
+        beforeScript = "$workflow.projectDir/src/conda_psmn.sh"
         conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-- 
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