profiles { docker { docker.temp = "auto" docker.enabled = true process { withName: build_synthetic_bed { container = "lbmc/bedtools:2.25.0" cpus = 1 } withName: fasta_from_bed { container = "lbmc/bedtools:2.25.0" cpus = 1 } withName: index_fasta { container = "lbmc/bowtie2:2.3.4.1" cpus = 4 } withName: mapping_fastq_paired { container = "lbmc/bowtie2:2.3.4.1" cpus = 4 } withName: bam_2_fastq_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: filter_bam_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: sort_bam_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: index_bam_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: mapping_fastq_single { container = "lbmc/bowtie2:2.3.4.1" cpus = 4 } withName: bam_2_fastq_single { container = "lbmc/samtools:1.7" cpus = 4 } withName: filter_bam_single { container = "lbmc/samtools:1.7" cpus = 4 } withName: sort_bam_single { container = "lbmc/samtools:1.7" cpus = 4 } withName: index_bam_single { container = "lbmc/samtools:1.7" cpus = 4 } } } singularity { singularity.enabled = true singularity.cacheDir = "./bin/" process { withName: build_synthetic_bed { container = "lbmc/bedtools:2.25.0" cpus = 1 } withName: fasta_from_bed { container = "lbmc/bedtools:2.25.0" cpus = 1 } withName: index_fasta { container = "lbmc/bowtie2:2.3.4.1" cpus = 4 } withName: mapping_fastq_single { container = "lbmc/bowtie2:2.3.4.1" cpus = 4 } withName: mapping_fastq_paired { container = "lbmc/bowtie2:2.3.4.1" cpus = 4 } withName: bam_2_fastq_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: filter_bam_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: sort_bam_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: index_bam_paired { container = "lbmc/samtools:1.7" cpus = 4 } withName: bam_2_fastq_single { container = "lbmc/samtools:1.7" cpus = 4 } withName: filter_bam_single { container = "lbmc/samtools:1.7" cpus = 4 } withName: sort_bam_single { container = "lbmc/samtools:1.7" cpus = 4 } withName: index_bam_single { container = "lbmc/samtools:1.7" cpus = 4 } } } psmn { process{ withName: build_synthetic_bed { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bedtools_2.25.0" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 1 memory = "20GB" time = "12h" queue = "monointeldeb128" } withName: fasta_from_bed { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bedtools_2.25.0" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 1 memory = "20GB" time = "12h" queue = "monointeldeb128" } withName: index_fasta { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "20GB" time = "12h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: mapping_fastq_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: bam_2_fastq_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: sort_bam_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: index_bam_paired { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: mapping_fastq_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: bam_2_fastq_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: sort_bam_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } withName: index_bam_single { beforeScript = "source $baseDir/.conda_psmn.sh" conda = "$baseDir/.conda_envs/samtools_1.7" executor = "sge" clusterOptions = "-m e -cwd -V" cpus = 32 memory = "30GB" time = "24h" queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D" penv = "openmp32" } } } ccin2p3 { singularity.enabled = true singularity.cacheDir = "$baseDir/.singularity_in2p3/" singularity.runOptions = "--bind /pbs,/sps,/scratch" process{ withName: fasta_from_bed { container = "lbmc/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" } } process{ withName: build_synthetic_bed { container = "lbmc/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" } withName: fasta_from_bed { container = "lbmc/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" } withName: index_fasta { container = "lbmc/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" } withName: mapping_fastq_paired { container = "lbmc/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" } withName: bam_2_fastq_paired { container = "lbmc/samtools:1.7" 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: sort_bam_paired { container = "lbmc/samtools:1.7" 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: index_bam_paired { container = "lbmc/samtools:1.7" 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: mapping_fastq_single { container = "lbmc/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" } withName: bam_2_fastq_single { container = "lbmc/samtools:1.7" 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: sort_bam_single { container = "lbmc/samtools:1.7" 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: index_bam_single { container = "lbmc/samtools:1.7" scratch = true stageInMode = "copy" stageOutMode = "rsync" executor = "sge" clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n" cpus = 1 queue = "huge" } } } }