From e170dad3744588f42b46c4af8f13e8fccbe3f40e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 20 May 2019 16:36:36 +0200
Subject: [PATCH] nf modules: add ccin2p3 profile

---
 src/nf_modules/bedtools/fasta_from_bed.config | 17 +++++++
 src/nf_modules/bowtie/indexing.config         | 17 +++++++
 src/nf_modules/bowtie/mapping_paired.config   | 17 +++++++
 src/nf_modules/bowtie/mapping_single.config   | 17 +++++++
 src/nf_modules/bowtie2/indexing.config        | 17 +++++++
 src/nf_modules/bowtie2/mapping_paired.config  | 17 +++++++
 src/nf_modules/bowtie2/mapping_single.config  | 17 +++++++
 src/nf_modules/bwa/indexing.config            | 17 +++++++
 src/nf_modules/bwa/mapping_paired.config      | 17 +++++++
 .../cutadapt/adaptor_removal_paired.config    | 17 +++++++
 .../cutadapt/adaptor_removal_single.config    | 17 +++++++
 .../cutadapt/trimming_paired.config           | 17 +++++++
 .../cutadapt/trimming_single.config           | 17 +++++++
 src/nf_modules/deeptools/bam_to_bigwig.config | 30 +++++++++++-
 .../deeptools/compute_matrix.config           | 17 +++++++
 src/nf_modules/deeptools/plot_profile.config  | 17 +++++++
 src/nf_modules/fastp/fastp_paired.config      | 17 +++++++
 src/nf_modules/fastp/fastp_single.config      | 17 +++++++
 src/nf_modules/fastqc/fastqc_paired.config    | 17 +++++++
 src/nf_modules/fastqc/fastqc_single.config    | 17 +++++++
 src/nf_modules/hisat2/indexing.config         | 17 +++++++
 src/nf_modules/hisat2/mapping_paired.config   | 17 +++++++
 src/nf_modules/hisat2/mapping_single.config   | 17 +++++++
 src/nf_modules/htseq/htseq.config             | 17 +++++++
 src/nf_modules/kallisto/mapping_paired.config | 17 +++++++
 src/nf_modules/kallisto/mapping_single.config | 17 +++++++
 src/nf_modules/macs2/peak_calling.config      | 17 +++++++
 src/nf_modules/multiqc/multiqc_paired.config  | 17 +++++++
 src/nf_modules/multiqc/multiqc_single.config  | 17 +++++++
 .../music/peak_calling_single.config          | 46 ++++++-------------
 src/nf_modules/rsem/indexing.config           | 17 +++++++
 .../rsem/quantification_paired.config         | 17 +++++++
 .../rsem/quantification_single.config         | 17 +++++++
 src/nf_modules/sambamba/index_bams.config     | 17 +++++++
 src/nf_modules/sambamba/sort_bams.config      | 17 +++++++
 src/nf_modules/sambamba/split_bams.config     | 17 +++++++
 src/nf_modules/samblaster/dedup_sams.config   | 17 +++++++
 src/nf_modules/samtools/filter_bams.config    | 17 +++++++
 src/nf_modules/samtools/index_bams.config     | 17 +++++++
 src/nf_modules/samtools/sort_bams.config      | 17 +++++++
 src/nf_modules/samtools/split_bams.config     | 17 +++++++
 src/nf_modules/sratoolkit/fastqdump.config    | 17 +++++++
 src/nf_modules/urqt/trimming_paired.config    | 17 +++++++
 src/nf_modules/urqt/trimming_single.config    | 17 +++++++
 44 files changed, 756 insertions(+), 34 deletions(-)

diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 36e7ef4..220cdce 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 19094c4..e1b0262 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 7e00b2b..d24ba5d 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 7e00b2b..d24ba5d 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 8a373d9..98b7cda 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 704adb6..7d8e543 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 704adb6..7d8e543 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index d73ff10..89574aa 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 1c8dfa5..4f01360 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 7e6aade..7317fb7 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 7e6aade..7317fb7 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 28e1728..f201a57 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 28e1728..f201a57 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index e6d7134..67a46dc 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 0000f5b..66be28d 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index afa10d5..bb1feb2 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index f660e79..67af9be 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index f660e79..67af9be 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 291d2eb..70c9b99 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 291d2eb..70c9b99 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index fc8ca47..c3784d3 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 31edc5c..993ef10 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 31edc5c..993ef10 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index e703516..7349c5f 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 755a49b..2599af5 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/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'
+      }
+    }
+  }
 }
 
 
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 755a49b..2599af5 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/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'
+      }
+    }
+  }
 }
 
 
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 43e5cbe..d5223cd 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 4413a1e..813b55e 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/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'
+      }
+    }
+  }
 }
 
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 451cbd2..304ea3e 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index b941875..64a55bd 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/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"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d551058..1149d29 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 7a31107..3519333 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 7a31107..3519333 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 4b1cab9..7055c98 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 20a878c..2ccdc38 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index ed57b76..57346f1 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index a4ed173..6911ff9 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 8b6406f..0116e7c 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 9b37acf..dfab8d3 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 6f55fb1..45c69f8 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 7d8c883..f03bc1a 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 3bfdaae..1538b1a 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.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'
+      }
+    }
+  }
 }
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 143b4b1..2073efc 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -49,5 +49,22 @@ 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'
+      }
+    }
+  }
 }
 
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index c787338..e82bd35 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -49,5 +49,22 @@ 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'
+      }
+    }
+  }
 }
 
-- 
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