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test_cases.txt
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test_cases.txt
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snakemake -pj 10 --configfile inputs.json --snakefile snakyVC.smk
snakemake -pj 10 --configfile chromosomewise_inputs.json --snakefile snakyVC_chromosomewise.smk
snakemake -pj 10 --configfile workflow_inputs/BWA_alignment_to_GATK_HaplotypeCaller_inputs.json \
--snakefile workflows/BWA_alignment_to_GATK_HaplotypeCaller.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_CombineGVCFs_to_GATK_SelectVariants_inputs.json \
--snakefile workflows/GATK_CombineGVCFs_to_GATK_SelectVariants.smk
snakemake -pj 10 --configfile workflow_inputs/BWA_alignment_to_GATK_AddOrReplaceReadGroups_inputs.json \
--snakefile workflows/BWA_alignment_to_GATK_AddOrReplaceReadGroups.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_HaplotypeCaller_inputs.json \
--snakefile workflows/GATK_HaplotypeCaller.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_CombineGVCFs_to_GATK_SelectVariants_chromosomewise_inputs.json \
--snakefile workflows/GATK_CombineGVCFs_to_GATK_SelectVariants_chromosomewise.smk
snakemake -pj 10 --configfile workflow_inputs/BWA_alignment_to_GATK_AddOrReplaceReadGroups_inputs.json \
--snakefile workflows/BWA_alignment_to_GATK_AddOrReplaceReadGroups.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_HaplotypeCaller_inputs.json \
--snakefile workflows/GATK_HaplotypeCaller.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_CombineGVCFs_inputs.json \
--snakefile workflows/GATK_CombineGVCFs.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_GenotypeGVCFs_to_GATK_SelectVariants_inputs.json \
--snakefile workflows/GATK_GenotypeGVCFs_to_GATK_SelectVariants.smk
snakemake -pj 10 --configfile workflow_inputs/BWA_alignment_to_GATK_AddOrReplaceReadGroups_inputs.json \
--snakefile workflows/BWA_alignment_to_GATK_AddOrReplaceReadGroups.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_HaplotypeCaller_inputs.json \
--snakefile workflows/GATK_HaplotypeCaller.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_CombineGVCFs_chromosomewise_inputs.json \
--snakefile workflows/GATK_CombineGVCFs_chromosomewise.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_GenotypeGVCFs_to_GATK_SelectVariants_chromosomewise_inputs.json \
--snakefile workflows/GATK_GenotypeGVCFs_to_GATK_SelectVariants_chromosomewise.smk
snakemake -pj 10 --configfile workflow_inputs/BWA_alignment_to_GATK_AddOrReplaceReadGroups_inputs.json \
--snakefile workflows/BWA_alignment_to_GATK_AddOrReplaceReadGroups.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_HaplotypeCaller_to_GATK_SelectVariants_chromosomewise_inputs.json \
--snakefile workflows/GATK_HaplotypeCaller_to_GATK_SelectVariants_chromosomewise.smk
snakemake -pj 10 --configfile workflow_inputs/BWA_alignment_single_inputs.json \
--snakefile workflows/BWA_alignment_single.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_SortSam_to_GATK_SelectVariants_inputs.json \
--snakefile workflows/GATK_SortSam_to_GATK_SelectVariants.smk
snakemake -pj 10 --configfile workflow_inputs/BWA_alignment_single_inputs.json \
--snakefile workflows/BWA_alignment_single.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_SortSam_to_GATK_AddOrReplaceReadGroups_inputs.json \
--snakefile workflows/GATK_SortSam_to_GATK_AddOrReplaceReadGroups.smk
snakemake -pj 10 --configfile workflow_inputs/GATK_MarkDuplicates_to_GATK_SelectVariants_inputs.json \
--snakefile workflows/GATK_MarkDuplicates_to_GATK_SelectVariants.smk
snakemake -pj 10 --configfile lewis_slurm_inputs.json --snakefile snakyVC.smk
snakemake -pj 10 --configfile lewis_slurm_chromosomewise_inputs.json --snakefile snakyVC_chromosomewise.smk
snakemake --executor cluster-generic \
--cluster-generic-submit-cmd "sbatch --account=xulab \
--partition=Lewis,BioCompute,hpc5,General --mem=16G" \
--jobs 30 --latency-wait 180 --configfile lewis_slurm_inputs.json \
--snakefile snakyVC.smk
snakemake --executor cluster-generic \
--cluster-generic-submit-cmd "sbatch --account=xulab \
--partition=Lewis,BioCompute,hpc5,General --mem=16G" \
--jobs 30 --latency-wait 3600 --immediate-submit --notemp \
--configfile lewis_slurm_inputs.json --snakefile snakyVC.smk
nohup snakemake --executor cluster-generic \
--cluster-generic-submit-cmd "sbatch --account=xulab \
--partition=Lewis,BioCompute,hpc5,General --mem=16G" \
--jobs 30 --latency-wait 3600 \
--configfile lewis_slurm_inputs.json --snakefile snakyVC.smk &