Commit 38a79de4 authored by Spencer Barnes's avatar Spencer Barnes
Browse files

remove superfluous comment lines and fix biohpc config

parent ef80fc4e
Pipeline #7501 failed with stages
in 813 minutes and 18 seconds
......@@ -14,24 +14,20 @@ process {
withName: trimReads {
module = ['python/3.6.1-2-anaconda', 'trimgalore/0.4.1']
cpus = 32
//queue = 'super'
queue = '128GB,256GB,256GBv1'
}
withName: alignReads{
module = ['python/3.6.1-2-anaconda', 'hisat2/2.1.0-intel', 'bismark/0.21.0', 'samtools/1.6', 'bowtie2/gcc/2.3.4.3']
queue = '128GB,256GB,256GBv1'
//queue = 'super'
}
withName: methylExtract{
module = ['python/3.6.1-2-anaconda', 'bismark/0.21.0', 'samtools/1.6']
queue = '128GB,256GB,256GBv1'
//queue = 'super'
}
withName: diffMeth{
module = ['R/3.5.1-gccmkl', 'python/3.6.1-2-anaconda']
queue = '128GB,256GB,256GBv1'
//queue = 'super'
}
withName: multiqcReport{
......@@ -41,30 +37,6 @@ process {
}
//params {
// // Reference file paths on BioHPC
// genomes {
// 'GRCh38' {
// bwa = '/project/shared/bicf_workflow_ref/GRCh38'
// genomesize = 'hs'
// chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
// fasta = '/project/shared/bicf_workflow_ref/GRCh38/genome.fa'
// }
// 'GRCh37' {
// bwa = '/project/shared/bicf_workflow_ref/GRCh37'
// genomesize = 'hs'
// chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
// fasta = '/project/shared/bicf_workflow_ref/GRCh37/genome.fa'
// }
// 'GRCm38' {
// bwa = '/project/shared/bicf_workflow_ref/GRCm38'
// genomesize = 'mm'
// chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
// fasta = '/project/shared/bicf_workflow_ref/GRCm38/genome.fa'
// }
// }
//}
trace {
enabled = true
file = 'pipeline_trace.txt'
......
......@@ -43,13 +43,7 @@ process trackStart {
params.output = "$baseDir"
params.designFile = "$baseDir/../test_data/test_design_se.csv"
params.pairedEnd = false
//params.reads = "$baseDir/../test_data/single/*.fastq.gz"
params.reads = "/work/BICF/s181385/methylation_test_data/shortened/paired/*.fastq.gz"
//params.reads = "/work/BICF/s181385/methylation_test_data/shortened/single/*.fastq.gz"
//params.reads = "/work/BICF/s181385/test_again/*.fastq.gz"
//params.reads = "/work/BICF/s181385/methylation_test_data/paired/*.fastq.gz"
//params.reads = "/work/BICF/s181385/methylation_test_data/single/*.fastq.gz"
//params.reads = "/project/BICF/BICF_Core/shared/bicf_collaborations/effort240_MunshiNi/data/bennett_data/*.fastq.gz"
params.rrbs = true
params.enzyme = "Msp1"
params.genome = "GRCm38"
......@@ -126,8 +120,7 @@ rawReads = designFilePaths
//Trim reads using trimgalore
process trimReads {
queue "super"
//queue "128GB,256GB,256GBv1"
queue "128GB,256GB,256GBv1"
tag "$sampleId-$replicate"
publishDir "$outDir/${task.process}/${sampleId}", mode: "copy"
......
......@@ -139,7 +139,7 @@ def trim_reads(fastq, paired, bismark, enzyme):
trim_command = "trim_galore %s %s %s " \
% (trim_params, fastq[0], fastq[1])
else:
raise Exception("You done messed up A-a-ron!")
raise Exception("Enzyme not found!")
else:
if enzyme == "Msp1":
......@@ -151,7 +151,7 @@ def trim_reads(fastq, paired, bismark, enzyme):
trim_command = "trim_galore %s %s " \
% (trim_params, fastq[0])
else:
raise Exception("You done messed up A-a-ron!")
raise Exception("Enzyme not found!")
else:
if paired: # paired-end data
trim_params = '--paired -q 25 --illumina --gzip --length 35'
......
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