nf_modules: switch psmn to singularity

src/nf_modules/samtools/split_bams.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: split_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/sratoolkit/fastqdump.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastq_dump {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
+        container = "lbmc/sratoolkit:2.8.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/star/indexing.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/star_2.7.3a"
+        container = "lbmc/star:2.7.3a"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/star/mapping_paired.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/star_2.7.3a"
+        container = "lbmc/star:2.7.3a"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/star/mapping_single.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/star_2.7.3a"
+        container = "lbmc/star:2.7.3a"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/subread/subread.config

@@ -28,20 +28,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: sort_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samtools_1.7"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: counting {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "subread/1.6.4"
+        container = "lbmc/subread:1.6.4"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/urqt/trimming_paired.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "5GB"

src/nf_modules/urqt/trimming_single.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+        container = "lbmc/urqt:d62c1f8"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/solution_RNASeq.config

@@ -52,64 +52,6 @@ profiles {
     }
   }
   psmn{
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/cutadapt_2.1"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: trimming {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 32
-        memory = "30GB"
-        time = "24h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
-        penv = "openmp32"
-
-      }
-      withName: fasta_from_bed {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: index_fasta {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 32
-        memory = "30GB"
-        time = "24h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
-        penv = "openmp32"
-      }
-      withName: mapping_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 32
-        memory = "30GB"
-        time = "24h"
-        queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
-        penv = "openmp32"
-      }
-    }
-  }
-  psmn_singularity{
     singularity.enabled = true
     singularity.cacheDir = "$baseDir/.singularity_psmn/"
     singularity.runOptions = "--bind /Xnfs,/scratch"