nf: change psmn config to use conda

src/nf_modules/samtools/split_bams.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: split_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/sratoolkit/fastqdump.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fastq_dump {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sratoolkit/2.8.2"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "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 = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "samtools/1.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "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 = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "urqt/d62c1f8"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "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 = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "urqt/d62c1f8"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "urqt_d62c1f8"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16