training_dataset.config: update conda_psmn.sh path to use $workflow

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"