diff --git a/src/RNAseq_sen1D_bowtie2_nosplit.config b/src/RNAseq_sen1D_bowtie2_nosplit.config new file mode 100644 index 0000000000000000000000000000000000000000..ce64be961cdc7d26d6c90829f672274056bb4cae --- /dev/null +++ b/src/RNAseq_sen1D_bowtie2_nosplit.config @@ -0,0 +1,143 @@ +profiles { + docker { + docker.temp = 'auto' + docker.enabled = true + process { + $fastqc_fastq { + container = "fastqc:0.11.5" + } + $fastqc_fastq_cutadapt { + container = "fastqc:0.11.5" + } + $fastqc_fastq_randombp { + container = "fastqc:0.11.5" + } + $fastqc_fastq_urqt { + container = "fastqc:0.11.5" + } + $adaptor_removal { + container = "cutadapt:1.14" + } + $multiqc { + container = "multiqc:1.0" + } + $random_bases_4_trimming { + container = "cutadapt:1.14" + } + $trimming { + container = "urqt:d62c1f8" + } + $index_fasta { + container = "bowtie2:2.3.4.1" + } + $mapping_fastq { + container = "bowtie2:2.3.4.1" + } + $sort_bam { + container = "samtools:1.7" + } + $index_bam { + container = "samtools:1.7" + } + } + } + sge { + process{ + $fastqc_fastq { + beforeScript = "module purge; module load FastQC/0.11.5" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'monointeldeb128' + } + $fastqc_fastq_cutadapt { + beforeScript = "module purge; module load FastQC/0.11.5" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'monointeldeb128' + } + $fastqc_fastq_randombp { + beforeScript = "module purge; module load FastQC/0.11.5" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'monointeldeb128' + } + $fastqc_fastq_urqt { + beforeScript = "module purge; module load FastQC/0.11.5" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'monointeldeb128' + } + $multiqc { + beforeScript = "module purge; module load FastQC/1.0" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'monointeldeb128' + } + $adaptor_removal { + beforeScript = "module purge; module load cutadapt/1.14" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'h6-E5-2667v4deb128' + penv = 'openmp8' + } + $random_bases_4_trimming { + beforeScript = "module purge; module load cutadapt/1.14" + executor = "sge" + cpus = 1 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'h6-E5-2667v4deb128' + penv = 'openmp8' + } + $trimming { + beforeScript = "module purge; module load UrQt/d62c1f8" + executor = "sge" + cpus = 4 + memory = "5GB" + time = "6h" + queueSize = 1000 + pollInterval = '60sec' + queue = 'h6-E5-2667v4deb128' + penv = 'openmp8' + } + $index_fasta { + beforeScript = "module purge; module load Bowtie2/2.3.4.1" + } + $mapping_fastq { + beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1" + } + $sort_bam { + beforeScript = "module purge; module load SAMtools/1.7" + } + $index_bam { + beforeScript = "module purge; module load SAMtools/1.7" + } + } + } +}