nf_modules: rm ccin2p3_conda section in config files

src/nf_modules/bedtools/fasta_from_bed.config

@@ -33,22 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fasta_from_bed {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bedtools_2.25.0"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bowtie/indexing.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bowtie/mapping_paired.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bowtie/mapping_single.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bowtie2/indexing.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bowtie2/mapping_paired.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bowtie2/mapping_single.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bwa/indexing.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_fasta {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/bwa/mapping_paired.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: mapping_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -33,22 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -33,22 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: adaptor_removal {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/cutadapt/trimming_paired.config

@@ -33,21 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/cutadapt/trimming_single.config

@@ -33,21 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: trimming {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/deeptools/bam_to_bigwig.config

@@ -53,34 +53,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: index_bam {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-      withName: bam_to_bigwig {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/deeptools/compute_matrix.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: compute_matrix {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/deeptools/plot_profile.config

@@ -34,22 +34,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: plot_profile {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/fastp/fastp_paired.config

@@ -33,22 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastp_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/fastp/fastp_single.config

@@ -33,22 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastp_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/fastqc/fastqc_paired.config

@@ -33,22 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"

src/nf_modules/fastqc/fastqc_single.config

@@ -33,22 +33,6 @@ profiles {
       }
     }
   }
-  ccin2p3_conda {
-    process{
-      withName: fastqc_fastq {
-        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
-        conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
-        scratch = true
-        stageInMode = "copy"
-        stageOutMode = "rsync"
-        executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
-        "
-        cpus = 1
-        queue = 'huge'
-      }
-    }
-  }
   ccin2p3 {
     singularity.enabled = true
     singularity.cacheDir = "/sps/lbmc/common/singularity/"