nf modules: add ccin2p3 profile

src/nf_modules/hisat2/indexing.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/hisat2/mapping_paired.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/hisat2/mapping_single.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/htseq/htseq.config

@@ -74,4 +74,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/kallisto/mapping_paired.config

@@ -49,6 +49,23 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }
 
 

src/nf_modules/kallisto/mapping_single.config

@@ -49,6 +49,23 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }
 
 

src/nf_modules/macs2/peak_calling.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/multiqc/multiqc_paired.config

@@ -83,5 +83,22 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }
 

src/nf_modules/multiqc/multiqc_single.config

@@ -82,4 +82,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/music/peak_calling_single.config

@@ -71,41 +71,18 @@ profiles {
   ccin2p3_conda {
     process{
       withName: compute_mappability {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/music/6613c53/:/usr/bin:$PATH"
+        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
         executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
       withName: music_preprocessing {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/music/6613c53/:/usr/bin:$PATH"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        memory = "10GB"
-        time = "24h"
-      }
-      withName: music_computation {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/music/6613c53/:/usr/bin:$PATH"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        memory = "10GB"
-        time = "24h"
-      }
-    }
-    process{
-      withName: compute_mappability {
         beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
         conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
         scratch = true
@@ -117,7 +94,7 @@ profiles {
         cpus = 1
         queue = 'huge'
       }
-      withName: music_preprocessing {
+      withName: music_computation {
         beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
         conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
         scratch = true
@@ -129,9 +106,14 @@ profiles {
         cpus = 1
         queue = 'huge'
       }
-      withName: music_computation {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
+    }
+  }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"

src/nf_modules/rsem/indexing.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/rsem/quantification_paired.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/rsem/quantification_single.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/sambamba/index_bams.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/sambamba/sort_bams.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/sambamba/split_bams.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/samblaster/dedup_sams.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/samtools/filter_bams.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/samtools/index_bams.config

@@ -48,4 +48,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }

src/nf_modules/samtools/sort_bams.config

@@ -49,4 +49,21 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_fasta {
+        container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
 }