Commit 5b66d32d authored by Spencer Barnes's avatar Spencer Barnes
Browse files

add parameters to astrocyte yml

parent 999e057d
Pipeline #7556 failed with stages
in 3 seconds
......@@ -40,6 +40,14 @@ documentation_files:
# Specify versioned module names to ensure reproducability.
workflow_modules:
- 'singularity/3.0.2'
- 'pandoc/2.7'
- 'python/3.6.1-2-anaconda'
- 'R/3.5.1-gccmkl'
- 'samtools/intel/1.3'
- 'bismark/0.21.0'
- 'bowtie2/gcc/2.3.4.3'
- 'hisat2/2.1.0-intel'
- 'trimgalore/0.4.1'
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
......@@ -82,6 +90,42 @@ workflow_parameters:
A design file listing the sample names with corresponding fastq files.
regex: ".*txt"
-id: reads
type: files
required: true
description: |
One or more input FASTQ files from an RRBS/WGBS experiment and a design
file with the link between the same file name and sample id
regex: ".*(fastq|fq)*gz"
min: 2
-id: genome
type: select
required: true
choices:
- [ 'GRCh38', 'Human GRCh38']
- [ 'GRCm38', 'Mouse GRCm38']
description: |
Reference species and genome used for alignment and subsequent analysis.
-id: pairedEnd
type: select
required: true
choices:
- [ 'true', 'true']
- [ 'false', 'false']
description: |
If Paired-end: True, if Single-end: False.
-id: enzyme
type: select
required: true
choices:
- [ 'Msp1', 'Msp1']
- [ 'other', 'other']
description: |
The digestion enzyme used in the RRBS experiment.
- id: astrocyte
type: select
choices:
......
......@@ -154,8 +154,7 @@ process trimReads {
//Align reads with Bismark
process alignReads {
queue "super"
//queue "128GB,256GB,256GBv1"
queue "128GB,256GB,256GBv1"
tag "$sampleId-$replicate"
publishDir "$outDir/${task.process}/${sampleId}", mode: "copy"
......@@ -173,7 +172,7 @@ process alignReads {
if (pairedEnd) {
"""
module load python/3.6.1-2-anaconda
module load samtools
module load samtools/intel/1.3
module load hisat2/2.1.0-intel
module load bismark/0.21.0
python3 $baseDir/scripts/align_reads_bismark.py -p -f ${reads[0]} ${reads[1]} -r $genome -a -s $sampleId
......@@ -182,7 +181,7 @@ process alignReads {
else {
"""
module load python/3.6.1-2-anaconda
module load samtools
module load samtools/intel/1.3
module load hisat2/2.1.0-intel
module load bismark/0.21.0
python3 $baseDir/scripts/align_reads_bismark.py -f $reads -r $genome -a -s $sampleId
......@@ -194,7 +193,7 @@ process alignReads {
if (pairedEnd) {
"""
module load python/3.6.1-2-anaconda
module load samtools
module load samtools/intel/1.3
module load bowtie2/gcc/2.3.4.3
module load bismark/0.21.0
python3 $baseDir/scripts/align_reads_bismark.py -p -f ${reads[0]} ${reads[1]} -r $genome -s $sampleId
......@@ -203,7 +202,7 @@ process alignReads {
else {
"""
module load python/3.6.1-2-anaconda
module load samtools
module load samtools/intel/1.3
module load bowtie2/gcc/2.3.4.3
module load bismark/0.21.0
python3 $baseDir/scripts/align_reads_bismark.py -f $reads -r $genome -s $sampleId
......@@ -213,8 +212,7 @@ process alignReads {
}
process methylExtract {
queue "super"
//queue "128GB,256GB,256GBv1"
queue "128GB,256GB,256GBv1"
tag "$sampleId-$replicate"
publishDir "$outDir/${task.process}/${sampleId}", mode: "copy"
//publishDir "$outDir/${task.process}/", mode: "copy"
......@@ -232,7 +230,7 @@ process methylExtract {
script:
"""
module load python/3.6.1-2-anaconda
module load samtools
module load samtools/intel/1.3
module load bismark/0.21.0
python3 $baseDir/scripts/methylation_extract.py -b $bams
......
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