conda_psmn: fix path of the scripts in configs files

src/nf_modules/sratoolkit/fastqdump.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fastq_dump {
-        beforeScript = "./src/conda_psmn.sh"
-        conda = "sratoolkit_2.8.2"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/subread/subread.config

@@ -30,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: sort_bam {
-        beforeScript = "./src/conda_psmn.sh"
-        conda = "samtools_1.7"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/urqt/trimming_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "./src/conda_psmn.sh"
-        conda = "urqt_d62c1f8"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "5GB"

src/nf_modules/urqt/trimming_single.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "./src/conda_psmn.sh"
-        conda = "urqt_d62c1f8"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/training_dataset.config

@@ -118,7 +118,7 @@ profiles {
   psmn {
     process{
       withName: build_synthetic_bed {
-        beforeScript = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.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 = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.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 = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.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 = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.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 = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -171,7 +171,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_paired {
-        beforeScript = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -182,7 +182,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_paired {
-        beforeScript = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -193,7 +193,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: mapping_fastq_single {
-        beforeScript = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.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 = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -215,7 +215,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: sort_bam_single {
-        beforeScript = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
@@ -226,7 +226,7 @@ profiles {
         penv = 'openmp16'
       }
       withName: index_bam_single {
-        beforeScript = "source $baseDir/conda_psmn.sh"
+        beforeScript = "source $baseDir/.conda_psmn.sh"
         conda = "$baseDir/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"