Mercurial > repos > mini > strelka
changeset 18:3c10d88b55ad
improved user interface
| author | mini |
|---|---|
| date | Wed, 15 Oct 2014 14:43:12 +0200 |
| parents | 8260a4188b08 |
| children | bddc6981a6a7 |
| files | lib/strelka_config_bwa_default.ini lib/strelka_config_eland_default.ini lib/strelka_config_isaac_default.ini strelka.xml strelka_wrapper.py |
| diffstat | 5 files changed, 505 insertions(+), 60 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/strelka_config_bwa_default.ini Wed Oct 15 14:43:12 2014 +0200 @@ -0,0 +1,139 @@ + +; +; User configuration options for Strelka somatic small-variant caller +; workflow: +; + +[user] + +; +; isSkipDepthFilters should be set to 1 to skip depth filtration for +; whole exome or other targeted sequencing data +; +isSkipDepthFilters = 0 + +; +; strelka will not accept input reads above this depth (they will be skipped +; until the depth drops below this value). Set this value <= 0 to disable +; this feature. Using this filter will bound memory usage given extremely high +; depth input, but may be problematic in high-depth targeted sequencing +; applications. +; +maxInputDepth = 10000 + +; +; If the depth filter is not skipped, all variants which occur at a +; depth greater than depthFilterMultiple*chromosome mean depth will be +; filtered out. +; +depthFilterMultiple = 3.0 + +; +; Somatic SNV calls are filtered at sites where greater than this +; fraction of basecalls have been removed by the mismatch density +; filter in either sample. +; +snvMaxFilteredBasecallFrac = 0.4 + +; +; Somatic SNV calls are filtered at sites where greater than this +; fraction of overlapping reads contain deletions which span the SNV +; call site. +; +snvMaxSpanningDeletionFrac = 0.75 + +; +; Somatic indel calls are filtered if they represent an expansion or +; contraction of a repeated pattern with a repeat count greater than +; indelMaxRefRepeat in the reference (ie. if indelMaxRefRepeat is 8, +; then the indel is filtered when it is an expansion/contraction of a +; homopolymer longer than 8 bases, a dinucleotide repeat longer than +; 16 bases, etc.) +; +indelMaxRefRepeat = 8 + +; +; Somatic indel calls are filtered if greater than this fraction of +; basecalls in a window extending 50 bases to each side of an indel's +; call position have been removed by the mismatch density filter. +; +indelMaxWindowFilteredBasecallFrac = 0.3 + +; +; Somatic indels are filtered if they overlap ’interrupted +; homopolymers’ greater than this length. The term 'interrupted +; homopolymer' is used to indicate the longest homopolymer which can +; be found intersecting or adjacent to the called indel when a single +; non-homopolymer base is allowed. +; +indelMaxIntHpolLength = 14 + +; +; prior probability of a somatic snv or indel +; +ssnvPrior = 0.000001 +sindelPrior = 0.000001 + +; +; probability of an snv or indel noise allele +; +; NB: in the calling model a noise allele is shared in tumor and +; normal samples, but occurs at any frequency. +; +ssnvNoise = 0.0000005 +sindelNoise = 0.000001 + +; +; Fraction of snv noise attributed to strand-bias. +; +; It is not recommended to change this setting. However, if it is +; essential to turn the strand bias penalization off, the following is +; recommended: +; Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5, +; (1) set ssnvNoiseStrandBiasFrac = 0 +; (2) divide the current ssnvNoise value by 2 +; +ssnvNoiseStrandBiasFrac = 0.5 + +; +; minimum MAPQ score for PE reads at tier1: +; +minTier1Mapq = 20 + +; +; minimum MAPQ score for PE and SE reads at tier2: +; +minTier2Mapq = 5 + +; +; Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are +; marked as filtered: +; +ssnvQuality_LowerBound = 15 + +; +; Somatic quality score (QSI_NT, NT=ref) below which somatic indels +; are marked as filtered: +; +sindelQuality_LowerBound = 30 + +; +; Optionally write out read alignments which were altered during the +; realignment step. At the completion of the workflow run, the +; realigned reads can be found in: +; +; ${ANALYSIS_DIR}/realigned/{normal,tumor}.realigned.bam +; +isWriteRealignedBam = 0 + +; +; Jobs are parallelized over segments of the reference genome no larger +; than this size: +; +binSize = 25000000 + +; +; Additional arguments passed to strelka. +; +extraStrelkaArguments = +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/strelka_config_eland_default.ini Wed Oct 15 14:43:12 2014 +0200 @@ -0,0 +1,140 @@ + +; +; User configuration options for Strelka somatic small-variant caller +; workflow: +; + +[user] + +; +; isSkipDepthFilters should be set to 1 to skip depth filtration for +; whole exome or other targeted sequencing data +; +isSkipDepthFilters = 0 + +; +; strelka will not accept input reads above this depth (they will be skipped +; until the depth drops below this value). Set this value <= 0 to disable +; this feature. Using this filter will bound memory usage given extremely high +; depth input, but may be problematic in high-depth targeted sequencing +; applications. +; +maxInputDepth = 10000 + +; +; If the depth filter is not skipped, all variants which occur at a +; depth greater than depthFilterMultiple*chromosome mean depth will be +; filtered out. +; +depthFilterMultiple = 3.0 + +; +; Somatic SNV calls are filtered at sites where greater than this +; fraction of basecalls have been removed by the mismatch density +; filter in either sample. +; +snvMaxFilteredBasecallFrac = 0.4 + +; +; Somatic SNV calls are filtered at sites where greater than this +; fraction of overlapping reads contain deletions which span the SNV +; call site. +; +snvMaxSpanningDeletionFrac = 0.75 + +; +; Somatic indel calls are filtered if they represent an expansion or +; contraction of a repeated pattern with a repeat count greater than +; indelMaxRefRepeat in the reference (ie. if indelMaxRefRepeat is 8, +; then the indel is filtered when it is an expansion/contraction of a +; homopolymer longer than 8 bases, a dinucleotide repeat longer than +; 16 bases, etc.) +; +indelMaxRefRepeat = 8 + +; +; Somatic indel calls are filtered if greater than this fraction of +; basecalls in a window extending 50 bases to each side of an indel's +; call position have been removed by the mismatch density filter. +; +indelMaxWindowFilteredBasecallFrac = 0.3 + +; +; Somatic indels are filtered if they overlap ’interrupted +; homopolymers’ greater than this length. The term 'interrupted +; homopolymer' is used to indicate the longest homopolymer which can +; be found intersecting or adjacent to the called indel when a single +; non-homopolymer base is allowed. +; +indelMaxIntHpolLength = 14 + +; +; prior probability of a somatic snv or indel +; +ssnvPrior = 0.000001 +sindelPrior = 0.000001 + +; +; probability of an snv or indel noise allele +; +; NB: in the calling model a noise allele is shared in tumor and +; normal samples, but occurs at any frequency. +; +ssnvNoise = 0.0000005 +sindelNoise = 0.0000001 + +; +; Fraction of snv noise attributed to strand-bias. +; +; It is not recommended to change this setting. However, if it is +; essential to turn the strand bias penalization off, the following is +; recommended: +; Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5, +; (1) set ssnvNoiseStrandBiasFrac = 0 +; (2) divide the current ssnvNoise value by 2 +; +ssnvNoiseStrandBiasFrac = 0.5 + +; +; minimum MAPQ score for PE reads at tier1: +; +minTier1Mapq = 40 + +; +; minimum MAPQ score for PE and SE reads at tier2: +; +minTier2Mapq = 5 + + +; +; Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are +; marked as filtered: +; +ssnvQuality_LowerBound = 15 + +; +; Somatic quality score (QSI_NT, NT=ref) below which somatic indels +; are marked as filtered: +; +sindelQuality_LowerBound = 30 + +; +; Optionally write out read alignments which were altered during the +; realignment step. At the completion of the workflow run, the +; realigned reads can be found in: +; +; ${ANALYSIS_DIR}/realigned/{normal,tumor}.realigned.bam +; +isWriteRealignedBam = 0 + +; +; Jobs are parallelized over segments of the reference genome no larger +; than this size: +; +binSize = 25000000 + +; +; Additional arguments passed to strelka. +; +extraStrelkaArguments = --eland-compatibility +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/strelka_config_isaac_default.ini Wed Oct 15 14:43:12 2014 +0200 @@ -0,0 +1,139 @@ + +; +; User configuration options for Strelka somatic small-variant caller +; workflow: +; + +[user] + +; +; isSkipDepthFilters should be set to 1 to skip depth filtration for +; whole exome or other targeted sequencing data +; +isSkipDepthFilters = 0 + +; +; strelka will not accept input reads above this depth (they will be skipped +; until the depth drops below this value). Set this value <= 0 to disable +; this feature. Using this filter will bound memory usage given extremely high +; depth input, but may be problematic in high-depth targeted sequencing +; applications. +; +maxInputDepth = 10000 + +; +; If the depth filter is not skipped, all variants which occur at a +; depth greater than depthFilterMultiple*chromosome mean depth will be +; filtered out. +; +depthFilterMultiple = 3.0 + +; +; Somatic SNV calls are filtered at sites where greater than this +; fraction of basecalls have been removed by the mismatch density +; filter in either sample. +; +snvMaxFilteredBasecallFrac = 0.4 + +; +; Somatic SNV calls are filtered at sites where greater than this +; fraction of overlapping reads contain deletions which span the SNV +; call site. +; +snvMaxSpanningDeletionFrac = 0.75 + +; +; Somatic indel calls are filtered if they represent an expansion or +; contraction of a repeated pattern with a repeat count greater than +; indelMaxRefRepeat in the reference (ie. if indelMaxRefRepeat is 8, +; then the indel is filtered when it is an expansion/contraction of a +; homopolymer longer than 8 bases, a dinucleotide repeat longer than +; 16 bases, etc.) +; +indelMaxRefRepeat = 8 + +; +; Somatic indel calls are filtered if greater than this fraction of +; basecalls in a window extending 50 bases to each side of an indel's +; call position have been removed by the mismatch density filter. +; +indelMaxWindowFilteredBasecallFrac = 0.3 + +; +; Somatic indels are filtered if they overlap ’interrupted +; homopolymers’ greater than this length. The term 'interrupted +; homopolymer' is used to indicate the longest homopolymer which can +; be found intersecting or adjacent to the called indel when a single +; non-homopolymer base is allowed. +; +indelMaxIntHpolLength = 14 + +; +; prior probability of a somatic snv or indel +; +ssnvPrior = 0.000001 +sindelPrior = 0.000001 + +; +; probability of an snv or indel noise allele +; +; NB: in the calling model a noise allele is shared in tumor and +; normal samples, but occurs at any frequency. +; +ssnvNoise = 0.0000005 +sindelNoise = 0.000001 + +; +; Fraction of snv noise attributed to strand-bias. +; +; It is not recommended to change this setting. However, if it is +; essential to turn the strand bias penalization off, the following is +; recommended: +; Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5, +; (1) set ssnvNoiseStrandBiasFrac = 0 +; (2) divide the current ssnvNoise value by 2 +; +ssnvNoiseStrandBiasFrac = 0.5 + +; +; minimum MAPQ score for PE reads at tier1: +; +minTier1Mapq = 20 + +; +; minimum MAPQ score for PE and SE reads at tier2: +; +minTier2Mapq = 0 + +; +; Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are +; marked as filtered: +; +ssnvQuality_LowerBound = 15 + +; +; Somatic quality score (QSI_NT, NT=ref) below which somatic indels +; are marked as filtered: +; +sindelQuality_LowerBound = 30 + +; +; Optionally write out read alignments which were altered during the +; realignment step. At the completion of the workflow run, the +; realigned reads can be found in: +; +; ${ANALYSIS_DIR}/realigned/{normal,tumor}.realigned.bam +; +isWriteRealignedBam = 0 + +; +; Jobs are parallelized over segments of the reference genome no larger +; than this size: +; +binSize = 25000000 + +; +; Additional arguments passed to strelka. +; +extraStrelkaArguments = --remap-input-softclip +
--- a/strelka.xml Wed Oct 01 13:45:33 2014 +0200 +++ b/strelka.xml Wed Oct 15 14:43:12 2014 +0200 @@ -6,9 +6,19 @@ <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="0.1.11">vcftools</requirement> </requirements> - <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile - #if $configuration.configuration_switch == 'Default': - --configFile Default + <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam + #if $genomeSource.refGenomeSource == "history": + --refFile "${genomeSource.ownFile}" + #else: + --refFile "${genomeSource.index.fields.path}" + #end if + + #if $configuration.configuration_switch == 'Default for Bwa': + --configFile strelka_config_bwa_default.ini + #else if $configuration.configuration_switch == 'Default for Isaac': + --configFile strelka_config_isaac_default.ini + #else if $configuration.configuration_switch == 'Default for Eland': + --configFile strelka_config_eland_default.ini #else if $configuration.configuration_switch == 'Path': --configFile $configuration.configFile #else: @@ -40,13 +50,28 @@ </command> <inputs> - <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/> - <param format="bam" name="normalBam" type="data" label="Normal bam file"/> - <param format="fasta" name="refFile" type="data" label="ref fasta file"/> + <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/> + <param format="bam" name="normalBam" type="data" label="Normal bam file"/> + <conditional name="genomeSource"> + <param name="refGenomeSource" type="select" label="Choose the reference genome"> + <option value="cached">Built-in genome</option> + <option value="history">use a genome (fasta format) from history</option> + </param> + <when value="cached"> + <param name="index" type="select" label="Select a built-in reference genome" help="This list contains genomes cached at this Galaxy instance. If your genome of interest is not present here request it by using 'Help' link at the top of Galaxy interface or use the 'Use a genome (fasta format) from my history' option of the 'Select Reference Genome' dropdown."> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param format="fasta" name="ownFile" type="data" metadata_name="dbkey" label="Using reference file" help="This option works best for relatively small genomes. If you are working with large human-sized genomes, send request to Galaxy team for adding your reference to this Galaxy instance by using 'Help' link at the top of Galaxy interface."/> + </when> + </conditional> <conditional name="configuration"> <param name="configuration_switch" type="select" label="how do you want to configure strelka"> - <option value="Default" selected="true">Default</option> + <option value="Default for Bwa" selected="true">Default for Bwa</option> + <option value="Default for Eland">Default for Eland</option> + <option value="Default for Isaac">Default for Isaac</option> <option value="Path">Use a config file</option> <option value="Custom">Custom</option> </param> @@ -57,25 +82,27 @@ <param format="ini" name="configFile" type="data" label="config file"/> </when> <when value="Custom"> - <param name="binSize" type="integer" value="25000000" label="binSize" /> - <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" /> - <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" /> - <param name="isWriteRealignedBam" type="integer" value="0" min="0" max="1" label="isWriteRealignedBam" help="0 for no alignment else 1"/> - <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" /> - <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" /> - <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" /> - <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" /> - <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" /> - <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" /> - <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" /> - <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" /> - <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" /> - <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" /> - <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" /> - <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" /> - <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" /> - <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" /> - <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" /> + <param name="binSize" type="integer" value="25000000" label="binSize" help="Jobs are parallelized over segments of the reference genome no larger than this size:"/> + <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40, minimum MAPQ score for PE reads at tier1:" label="minTier1Mapq" /> + <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5, minimum MAPQ score for PE and SE reads at tier2:" label="minTier2Mapq" /> + <param name="isWriteRealignedBam" type="boolean" checked="false" truevalue="1" falsevalue="0" label="isWriteRealignedBam" help="Optionally write out read alignments which were altered during the realignment step. At the completion of the workflow run, the realigned reads can be found in:"/> + <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" help="prior probability of a somatic snv or indel"/> + <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" help="prior probability of a somatic snv or indel"/> + <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" help="probability of an snv or indel noise allele NB: in the calling model a noise allele is shared in tumor and normal samples, but occurs at any frequency."/> + <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" help="probability of an snv or indel noise allele NB: in the calling model a noise allele is shared in tumor and normal samples, but occurs at any frequency."/> + <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" help="Fraction of snv noise attributed to strand-bias. It is not recommended to change this setting. However, if it is essential to turn the strand bias penalization off, the following is recommended: Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5, + (1) set ssnvNoiseStrandBiasFrac = 0 + (2) divide the current ssnvNoise value by 2"/> + <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" help="Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are marked as filtered:"/> + <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" help="Somatic quality score (QSI_NT, NT=ref) below which somatic indels are marked as filtered:"/> + <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" help="isSkipDepthFilters should be set to 1 to skip depth filtration for whole exome or other targeted sequencing data"/> + <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" help="If the depth filter is not skipped, all variants which occur at a depth greater than depthFilterMultiple*chromosome mean depth will be filtered out."/> + <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" help="Somatic SNV calls are filtered at sites where greater than this fraction of basecalls have been removed by the mismatch density filter in either sample."/> + <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" help="Somatic SNV calls are filtered at sites where greater than this fraction of overlapping reads contain deletions which span the SNV call site."/> + <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" help="Somatic indel calls are filtered if they represent an expansion or contraction of a repeated pattern with a repeat count greater than indelMaxRefRepeat in the reference (ie. if indelMaxRefRepeat is 8, then the indel is filtered when it is an expansion/contraction of a homopolymer longer than 8 bases, a dinucleotide repeat longer than 16 bases, etc.)"/> + <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" help="Somatic indel calls are filtered if greater than this fraction of basecalls in a window extending 50 bases to each side of an indel's call position have been removed by the mismatch density filter."/> + <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" help="Somatic indels are filtered if they overlap ’interrupted homopolymers’ greater than this length. The term 'interrupted homopolymer' is used to indicate the longest homopolymer which can be found intersecting or adjacent to the called indel when a single non-homopolymer base is allowed."/> + <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" help="strelka will not accept input reads above this depth (they will be skipped until the depth drops below this value). Set this value <= 0 to disable this feature. Using this filter will bound memory usage given extremely high depth input, but may be problematic in high-depth targeted sequencing applications."/> <conditional name="extra_arguments"> <param name="extra_arguments_switch" type="select" label="Do you Want to add extraStrelkaArguments?"> <option value="No" selected="true">No</option> @@ -85,18 +112,18 @@ <!-- do nothing --> </when> <when value="Yes"> - <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" /> + <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" help="Additional arguments passed to strelka."/> </when> </conditional> </when> </conditional> - <param name="conf_file_check" type="boolean" label="output conf file" checked="False"/> - <param name="output1_file_check" type="boolean" label="output passed snvs(filtred)" checked="True"/> - <param name="output2_file_check" type="boolean" label="output passed indels(filtred)" checked="True"/> - <param name="output3_file_check" type="boolean" label="output all snvs" checked="True"/> - <param name="output4_file_check" type="boolean" label="output all indels" checked="True"/> - <param name="output5_file_check" type="boolean" label="normal realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/> - <param name="output6_file_check" type="boolean" label="tumor realigned bam" help="only if isWriteRealignedBam option is 1" checked="False"/> + <param name="conf_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/> + <param name="output1_file_check" type="boolean" label="passed snvs(filtred)" checked="True" help="Show filtred snvs"/> + <param name="output2_file_check" type="boolean" label="passed indels(filtred)" checked="True" help="Show filtred indels"/> + <param name="output3_file_check" type="boolean" label="all snvs" checked="True" help="Show snvs"/> + <param name="output4_file_check" type="boolean" label="all indels" checked="True" help="Show indels"/> + <param name="output5_file_check" type="boolean" label="Show normal realigned bam" help="only if isWriteRealignedBam option is checked" checked="False"/> + <param name="output6_file_check" type="boolean" label="Show tumor realigned bam" help="only if isWriteRealignedBam option is checked" checked="False"/> </inputs> @@ -139,7 +166,7 @@ <help> Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. -You can see more information at : https://sites.google.com/site/strelkasomaticvariantcaller +You can see more information at : https://sites.google.com/site/strelkasomaticvariantcaller. </help> </tool>
--- a/strelka_wrapper.py Wed Oct 01 13:45:33 2014 +0200 +++ b/strelka_wrapper.py Wed Oct 15 14:43:12 2014 +0200 @@ -61,30 +61,30 @@ print(os.environ['PATH']) parser = argparse.ArgumentParser() parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False ) - parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False ) - parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False ) - parser.add_argument( '-c', '--configFile', help='path to tumor bam file', required = False ) - parser.add_argument( '--depthFilterMultiple', help='path to tumor bam file', required = False ) - parser.add_argument( '--snvMaxFilteredBasecallFrac', help='path to tumor bam file', required = False ) - parser.add_argument( '--snvMaxSpanningDeletionFrac', help='path to tumor bam file', required = False ) - parser.add_argument( '--indelMaxRefRepeat', help='path to tumor bam file', required = False ) - parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='path to tumor bam file', required = False ) - parser.add_argument( '--indelMaxIntHpolLength', help='path to tumor bam file', required = False ) - parser.add_argument( '--ssnvPrior', help='path to tumor bam file', required = False ) - parser.add_argument( '--sindelPrior', help='path to tumor bam file', required = False ) - parser.add_argument( '--ssnvNoise', help='path to tumor bam file', required = False ) - parser.add_argument( '--sindelNoise', help='path to tumor bam file', required = False ) - parser.add_argument( '--ssnvNoiseStrandBiasFrac', help='path to tumor bam file', required = False ) - parser.add_argument( '--minTier1Mapq', help='path to tumor bam file', required = False ) - parser.add_argument( '--minTier2Mapq', help='path to tumor bam file', required = False ) - parser.add_argument( '--ssnvQuality_LowerBound', help='path to tumor bam file', required = False ) - parser.add_argument( '--sindelQuality_LowerBound', help='path to tumor bam file', required = False ) - parser.add_argument( '--isWriteRealignedBam', help='path to tumor bam file', required = False ) + parser.add_argument( '-n', '--normalBam', help='', required = False ) + parser.add_argument( '-r', '--refFile', help='', required = False ) + parser.add_argument( '-c', '--configFile', help='', required = False ) + parser.add_argument( '--depthFilterMultiple', help='', required = False ) + parser.add_argument( '--snvMaxFilteredBasecallFrac', help='', required = False ) + parser.add_argument( '--snvMaxSpanningDeletionFrac', help='', required = False ) + parser.add_argument( '--indelMaxRefRepeat', help='', required = False ) + parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='', required = False ) + parser.add_argument( '--indelMaxIntHpolLength', help='', required = False ) + parser.add_argument( '--ssnvPrior', help='', required = False ) + parser.add_argument( '--sindelPrior', help='', required = False ) + parser.add_argument( '--ssnvNoise', help='', required = False ) + parser.add_argument( '--sindelNoise', help='', required = False ) + parser.add_argument( '--ssnvNoiseStrandBiasFrac', help='', required = False ) + parser.add_argument( '--minTier1Mapq', help='', required = False ) + parser.add_argument( '--minTier2Mapq', help='', required = False ) + parser.add_argument( '--ssnvQuality_LowerBound', help='', required = False ) + parser.add_argument( '--sindelQuality_LowerBound', help='', required = False ) + parser.add_argument( '--isWriteRealignedBam', help='', required = False ) parser.add_argument( '--binSize', help='path to tumor bam file', required = False ) - parser.add_argument( '--extraStrelkaArguments', help='path to tumor bam file', required = False ) - parser.add_argument( '--isSkipDepthFilters', help='path to tumor bam file', required = False ) - parser.add_argument( '--maxInputDepth', help='path to tumor bam file', required = False ) - parser.add_argument( '--scriptPath', help='path to tumor bam file', required = False ) + parser.add_argument( '--extraStrelkaArguments', help='', required = False ) + parser.add_argument( '--isSkipDepthFilters', help='', required = False ) + parser.add_argument( '--maxInputDepth', help='', required = False ) + parser.add_argument( '--scriptPath', help='', required = False ) args = parser.parse_args() root_dir= args.scriptPath @@ -115,8 +115,8 @@ #creating config file if needed if args.configFile == "Custom": _create_config(vars(args), config_ini) - elif args.configFile == "Default": - cmdbash="cp %s %s" % (root_dir + "/strelka_config.sample", config_ini) + elif args.configFile in ["strelka_config_bwa_default.ini", "strelka_config_isaac_default.ini", "strelka_config_eland_default.ini"]: + cmdbash="cp %s %s" % (root_dir + "/lib/" + args.configFile, config_ini) my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed") else: if not os.path.exists(args.configFile):