nf_modules: switch psmn to singularity

src/nf_modules/fastqc/fastqc_single.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
+        container = "lbmc/fastqc:0.11.5"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/hisat2/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/hisat2_2.1.0"
+        container = "lbmc/hisat2:2.1.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"

src/nf_modules/htseq/htseq.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 = "htseq/0.11.2"
+        container = "lbmc/htseq:0.11.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/kallisto/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/kallisto_0.44.0"
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/kallisto/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/kallisto_0.44.0"
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/kallisto/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/kallisto_0.44.0"
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/macs2/peak_calling.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: peak_calling {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/macs2_2.1.2"
+        container = "lbmc/macs2:2.1.2"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/multiqc/multiqc_paired.config

@@ -29,22 +29,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1.70
-        pollInterval = "60sec"
-        queue = "monointeldeb128"
-      }
-      withName: multiqc {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "multiqc/1.7"
+        container = "lbmc/multiqc:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/multiqc/multiqc_single.config

@@ -28,22 +28,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: fastqc_fastq {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/fastqc_0.11.5"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1.70
-        pollInterval = "60sec"
-        queue = "monointeldeb128"
-      }
-      withName: multiqc {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "multiqc/1.7"
+        container = "lbmc/multiqc:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/music/peak_calling_single.config

@@ -36,30 +36,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: compute_mappability {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/music_6613c53"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: music_preprocessing {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "music/6613c53"
-        executor = "sge"
-        clusterOptions = "-cwd -V"
-        cpus = 1
-        memory = "20GB"
-        time = "12h"
-        queue = "monointeldeb128"
-      }
-      withName: music_computation{
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "music/6613c53"
+        container = "lbmc/music:6613c53"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/rsem/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/rsem_1.3.0"
+        container = "lbmc/rsem:1.3.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/rsem/quantification_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/rsem_1.3.0"
+        container = "lbmc/rsem:1.3.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/rsem/quantification_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/rsem_1.3.0"
+        container = "lbmc/rsem:1.3.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/sambamba/index_bams.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_bam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/sambamba_0.6.9"
+        container = "lbmc/sambamba:0.6.9"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/sambamba/sort_bams.config

@@ -20,10 +20,15 @@ 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/sambamba_0.6.9"
+        container = "lbmc/sambamba:0.6.9"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 4

src/nf_modules/sambamba/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/sambamba_0.6.9"
+        container = "lbmc/sambamba:0.6.9"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/samblaster/dedup_sams.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: dedup_sam {
-        beforeScript = "source $baseDir/.conda_psmn.sh"
-        conda = "$baseDir/.conda_envs/samblaster_0.1.24"
+        container = "lbmc/sambamba:0.6.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32

src/nf_modules/samtools/filter_bams.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: filter_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 = 32

src/nf_modules/samtools/index_bams.config

@@ -20,10 +20,15 @@ profiles {
     }
   }
   psmn{
+    singularity.enabled = true
+    singularity.cacheDir = "/.singularity_psmn/"
+    singularity.runOptions = "--bind /Xnfs,/scratch"
     process{
       withName: index_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/samtools/sort_bams.config

@@ -20,10 +20,15 @@ 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"
+        container = "lbmc/samtools:1.7"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 32