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Description
This workflow modifies the docker version of the OQFE workflow so that it can be executed on a cluster system using singularity. It addresses a few problems with the original pipeline, which is designed to be executed on a single server or virtual machine.
Running environment
This workflow is designed to be executed on a cluster system (SLURM, PBS etc) using singularity.
Code Snippets
20 21 | [ -f ${bin_dir}/oqfe_${oqfe_version}.sif ] || \ singularity pull docker://dnanexus/oqfe:${oqfe_version} |
23 24 | [ -f ${bin_dir}/deepvariant_${deep_variant_version}.sif ] || \ singularity pull docker://google/deepvariant:${deep_variant_version} |
26 27 | [ -f ${bin_dir}/deepvariant_${deep_variant_version}-gpu.sif ] || \ singularity pull docker://google/deepvariant:${deep_variant_version}-gpu |
55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | set -e mkdir -p ${work_dir} # singularity exec --home ${work_dir} -W ${work_dir} \ --bind "${source_dir}":/source_dir \ --bind "${reference_dir}":/reference_dir \ --bind "${bin_dir}":/oqfe_bin \ ${bin_dir}/oqfe_${oqfe_version}.sif python3.6 /oqfe_bin/oqfe_mem \ --forward-reads /source_dir/${_input:b} \ --num-cores 32 --memory 60000 \ --sample ${sample_id} --reuse-existing-outputs \ --cram-reference-fasta /reference_dir/GRCh38_full_analysis_set_plus_decoy_hla.fa # remove intermediate files, move output [ -f ${work_dir}/output/${sample_id}.oqfe.cram ] && mv ${work_dir}/output/* ${oqfe_output_dir} && rm -rf ${work_dir} |
86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 | mkdir -p ${deep_variant_output_dir} # https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md singularity run \ --bind "${source_dir}":/input \ --bind "${deep_variant_output_dir}":/output \ --bind "${reference_dir}":/reference \ --nv \ ${bin_dir}/deepvariant_${deep_variant_version}-gpu.sif \ /opt/deepvariant/bin/run_deepvariant \ --model_type WGS \ --ref /reference/GRCh38_full_analysis_set_plus_decoy_hla.fa \ --reads /input/${sample_id}.oqfe.cram \ --output_vcf /output/${sample_id}.output.vcf.gz \ --output_gvcf /output/${sample_id}.output.g.vcf.gz \ --num_shards 32 \ --intermediate_results_dir /output/intermediate_results_dir |
Support
Adapt the workflow for your environment.
The workflow is executed from a SoS workflow system on Jupyter Notebook. I can help run the workflow on your cluster.
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Files Included
- oqfe_pipeline_cluster.ipynb 10.2 kB
- oqfe_mem 24.5 kB
Created: 7mo ago
Updated: 7mo ago
Name:
oqfe-on-cluster
Version:
1
Accessed: 169
Downloaded:
1
Copyright:
Owned by public
License:
Non-Open License
Keywords:
Refs:
- Service available
- Future updates
- 30 day refund policy
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