nf modules: add ccin2p3 profile

src/nf_modules/bedtools/fasta_from_bed.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/bowtie/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/bowtie/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/bowtie/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/bowtie2/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/bowtie2/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/bowtie2/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/bwa/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/bwa/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/cutadapt/adaptor_removal_paired.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/cutadapt/adaptor_removal_single.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/cutadapt/trimming_paired.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/cutadapt/trimming_single.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/deeptools/bam_to_bigwig.config

@@ -66,8 +66,6 @@ profiles {
         cpus = 1
         queue = 'huge'
       }
-    }
-    process{
       withName: bam_to_bigwig {
         beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
         conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
@@ -82,4 +80,32 @@ profiles {
       }
     }
   }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: index_bam {
+        container = "/sps/lbmc/common/singularity/sambamba:0.6.7.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'
+      }
+      withName: bam_to_bigwig {
+        container = "/sps/lbmc/common/singularity/deeptools:3.0.2.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/deeptools/compute_matrix.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/deeptools/plot_profile.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/fastp/fastp_paired.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/fastp/fastp_single.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/fastqc/fastqc_paired.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/fastqc/fastqc_single.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'
+      }
+    }
+  }
 }