Commit b58a2175 authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

testing singularity

parent 6d3d64fe
Pipeline #9961 failed with stage
in 3 seconds
......@@ -161,6 +161,7 @@ workflow_parameters:
- [ '/project/shared/bicf_workflow_ref/human/GRCh38', 'Human GRCh38']
- [ '/project/shared/bicf_workflow_ref/human/GRCh37', 'Human GRCh37']
- [ '/project/shared/bicf_workflow_ref/mouse/GRCm38', 'Mouse GRCm38']
- [ '/project/shared/bicf_workflow_ref/mouse/GRCm39', 'Mouse GRCm39']
required: true
description: |
Reference genome for alignment
......
......@@ -6,32 +6,38 @@ process {
clusterOptions = '--hold --no-kill'
queue = '128GB,256GB,256GBv1'
withLabel: trim {
container = 'trim_galore.sif'
container = 'goalconsortium/trim_galore:1.0.9'
}
withLabel: dnaalign {
container = 'dna_alignment.sif'
withLabel: abra2 {
container = 'goalconsortium/abra2:1.0.9'
}
withLabel: profiling_qc {
container = 'profiling_qc.sif'
container = 'goalconsortium/profiling_qc:1.0.9'
}
withLabel: dnaalign {
container = 'goalconsortium/dna_alignment:1.0.9'
}
withLabel: variantcalling {
container = 'goalconsortium/variantcalling:1.0.9'
}
withLabel: structuralvariant {
container = 'goalconsortium/structuralvariant:1.1.2'
}
withLabel: starfusion {
container = 'starfusion.sif'
container = 'goalconsortium/starfusion:1.0.9'
}
withLabel: ralign {
container = 'rna_alignment.sif'
container = 'goalconsortium/rna_alignment:1.0.9'
}
withLabel: geneabund {
container = 'rna_gene_abundance.sif'
}
withLabel: rnaseqstat {
container = 'rnaseq_dea.sif'
container = 'goalconsortium/rna_gene_abundance:1.1.3'
}
}
singularity {
enabled = true
runOptions='--no-home --cleanenv'
cacheDir = '/project/shared/bicf_workflow_ref/seqprg/singularity/'
cacheDir="$PWD"
}
trace {
......@@ -57,9 +63,9 @@ env {
}
manifest {
homePage = 'https://git.biohpc.swmed.edu/ngsclialab/school'
description = 'School is a collection of genomics analysis workflows that are used for detecting single nucleotide variants (SNVs), insertions/deletions (indels), copy number variants (CNVs) and translocations from RNA and DNA sequencing. These workflows have been validated in a CLIA laboratory at UTSW'
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq'
description = 'RNA sequencing gene abundance analysi'
mainScript = 'rna.nf'
version = '1.0.0'
nextflowVersion = '>=0.31.0'
nextflowVersion = '>=20.01.0'
}
#!/bin/bash
module load nextflow/20.01.0 singularity/3.5.3
base='/project/BICF/BICF_Core/s166458/rnaseq_astrocyte'
datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
nextflow -C ${base}/nextflow.config run ${base}/workflow/main.nf --design ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis
#!/bin/bash
module load nextflow/20.01.0 singularity/3.5.3
base='/project/BICF/BICF_Core/s166458/rnaseq_astrocyte'
datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
nextflow -C ${base}/nextflow.config run -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html ${base}/workflow/main.nf --design ${datadir}/mouse_se.design.txt --input ${datadir} --pairs se --output analysis
#!/bin/bash
baseDir="`dirname \"$0\"`"
cd ${baseDir}/mouse_se_test/
sbatch -p 32GB,super run_test.sh
cd ${baseDir}/human_pe_test/
sbatch -p 32GB,super run_test.sh
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