nf_modules: update ccin2p3 config

src/nf_modules/bedtools/fasta_from_bed.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: fasta_from_bed {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bedtools/2.25.0/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bowtie/indexing.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: index_fasta {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bowtie/mapping_paired.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: mapping_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bowtie/mapping_single.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: mapping_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bowtie2/indexing.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: index_fasta {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bowtie2/mapping_paired.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: mapping_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bowtie2/mapping_single.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: mapping_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bwa/indexing.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: index_fasta {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/bwa/mapping_paired.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: mapping_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: adaptor_removal {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: adaptor_removal {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/cutadapt/trimming_paired.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: trimming {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/cutadapt/trimming_single.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: trimming {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/deeptools/bam_to_bigwig.config

@@ -55,28 +55,30 @@ profiles {
   ccin2p3 {
     process{
       withName: index_bam {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+        beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+        conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
         scratch = true
         stageInMode = "copy"
         stageOutMode = "rsync"
         executor = "sge"
-        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
     process{
       withName: bam_to_bigwig {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/deeptools/compute_matrix.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: compute_matrix {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/deeptools/plot_profile.config

@@ -36,15 +36,16 @@ profiles {
   ccin2p3 {
     process{
       withName: plot_profile {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/fastp/fastp_paired.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: fastp_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastp/0.19.7/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/fastp/fastp_single.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: fastp_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastp/0.19.7/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/fastqc/fastqc_paired.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: fastqc_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }

src/nf_modules/fastqc/fastqc_single.config

@@ -35,15 +35,16 @@ profiles {
   ccin2p3 {
     process{
       withName: fastqc_fastq {
-        beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+        beforeScript = "sh /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"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+        -o ~/logs/ -e ~/logs/"
         cpus = 1
-        memory = "10GB"
-        time = "24h"
+        queue = 'huge'
       }
     }
   }