Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/strelka_somatic/strelka_somatic/2.9.10+galaxy0 (this tool) |
strelka_somatic |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
strelka | 2.9.10 | package |
samtools | 1.9 | package |
Additional information about this tool |
## initialize #if $normalBam.is_of_type('bam') ln -s '$normalBam' './input_normal.bam' && ln -s '$normalBam.metadata.bam_index' './input_normal.bam.bai' && #elif $normalBam.is_of_type('cram') ln -s '$normalBam' './input_normal.cram' && ln -s '$normalBam.metadata.cram_index' './input_normal.cram.crai' && #end if #if $tumorBam.is_of_type('bam') ln -s '$tumorBam' './input_tumor.bam' && ln -s '$tumorBam.metadata.bam_index' './input_tumor.bam.bai' && #elif $tumorBam.is_of_type('cram') ln -s '$tumorBam' './input_tumor.cram' && ln -s '$tumorBam.metadata.cram_index' './input_tumor.cram.crai' && #end if ##ln -s '$referenceFasta' './input_ref.fasta' && ##samtools faidx './input_ref.fasta' && ## Make all optional regions files available ## Note: all of these must be tabixed #set $reg_options = [] #for $i, $sites in enumerate($forced_regions): #set $target_file = 'input_forcedgt_%d.vcf.gz' % $i #if $sites.whitelist.ext == 'vcf': bgzip -c '${sites.whitelist}' > $target_file && tabix -p vcf $target_file && #else: ln -s '${sites.whitelist}' $target_file && ln -s '${sites.whitelist.metadata.tabix_index}' ${target_file}.tbi' && #end if #if str($sites.use_whitelist_as) == 'indel_candidates': #silent $reg_options.extend(['--indelCandidates', $target_file]) #else: #silent $reg_options.extend(['--forcedGT', $target_file]) #end if #end for #if str($regions.restrict_to_region) == 'regions_from_file': #silent $reg_options.append('--callRegions') #set $target_file = 'input_callregions.bed.gz' #if $regions.callRegions.ext == 'bed': bgzip -c '$regions.callRegions' $target_file && tabix -p bed $target_file && else: ln -s '$regions.callRegions' $target_file && ln -s '$regions.callRegions.tabix_index' ${target_file}.tbi && #end if #silent $reg_options.append($target_file) #end if #set $region_spec = ' '.join($reg_options) #if str($ref_cond.ref_sel) == 'history': #set $reference_fasta_fn = 'input_ref.fasta' ln -s '$ref_cond.ref' $reference_fasta_fn && samtools faidx $reference_fasta_fn && #else #set $reference_fasta_fn = str($ref_cond.ref.fields.path) #end if ## create workflow configureStrelkaSomaticWorkflow.py #if $normalBam.is_of_type('bam') --normalBam ./input_normal.bam #elif $normalBam.is_of_type('cram') --normalBam ./input_normal.cram #end if #if $tumorBam.is_of_type('bam') --tumorBam ./input_tumor.bam #elif $tumorBam.is_of_type('cram') --tumorBam ./input_tumor.cram #end if $oo.outputCallableRegions --config='$config_file' $optimization #if str($expert_settings.evs.selector) == "disableEVS" --disableEVS #else #if $expert_settings.evs.snvScoringModelFile --snvScoringModelFile '$expert_settings.evs.snvScoringModelFile' #end if #if $expert_settings.evs.indelScoringModelFile --indelScoringModelFile '$expert_settings.evs.indelScoringModelFile' #end if $expert_settings.evs.reportEVSFeatures #end if $region_spec --referenceFasta '${reference_fasta_fn}' --runDir results && ## run workflow results/runWorkflow.py -m local -j \${GALAXY_SLOTS:-2} -g \${GALAXY_MEMORY_MB:-8192} ## decompress results if needed and move everything to final destinations #if $oo.vcf_type == "decompressed" && bgzip -d results/results/variants/somatic.indels.vcf.gz && bgzip -d results/results/variants/somatic.snvs.vcf.gz && mv results/results/variants/somatic.indels.vcf '$out_indels' && mv results/results/variants/somatic.snvs.vcf '$out_snvs' #else && mv results/results/variants/somatic.indels.vcf.gz '$out_indels' && mv results/results/variants/somatic.snvs.vcf.gz '$out_snvs' #end if #if $oo.outputCallableRegions && bgzip -d results/results/regions/somatic.callable.regions.bed.gz && mv results/results/regions/somatic.callable.regions.bed '$out_callable' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
normalBam: sample1.bam tumorBam: sample2.bam ref_cond|ref: hg98.fa ref_cond|ref_sel: history oo|vcf_type: False |
name: value name: value |
sample1.bam sample2.bam hg98.fa value |
Test-2 |
normalBam: sample1.cram tumorBam: sample2.cram ref_cond|ref: hg98.fa ref_cond|ref_sel: history oo|vcf_type: True |
name: value name: value |
sample1.cram sample2.cram hg98.fa value |
Test-3 |
normalBam: sample1.bam tumorBam: sample2.bam ref_cond|ref: hg98.fa ref_cond|ref_sel: history optimization: --exome oo|vcf_type: False oo|outputCallableRegions: True strelka|maxIndelSize: 50 strelka|depthFilterMultiple: 2.8 strelka|snvMaxFilteredBasecallFrac: 0.5 strelka|snvMaxSpanningDeletionFrac: 0.76 strelka|indelMaxWindowFilteredBasecallFrac: 0.4 strelka|ssnvPrior: 0.0002 strelka|sindelPrior: 0.000002 strelka|ssnvNoise: 0.0000000004 strelka|sindelNoiseFactor: 2.1 strelka|ssnvNoiseStrandBiasFrac: 0.1 strelka|minTier1Mapq: 21 strelka|minTier2Mapq: 1 strelka|ssnvQuality_LowerBound: 14 strelka|sindelQuality_LowerBound: 41 strelka|ssnvContamTolerance: 0.16 strelka|indelContamTolerance: 0.16 |
name: value name: value name: value |
sample1.bam sample2.bam hg98.fa value |
Test-4 |
normalBam: sample1.bam tumorBam: sample2.bam ref_cond|ref: hg19 ref_cond|ref_sel: cached oo|vcf_type: False |
name: value name: value |
sample1.bam sample2.bam value |