# HG changeset patch # User artbio # Date 1708417887 0 # Node ID 555971edd46e96a274f61ef7b8e00763bfc96576 # Parent cb5691381acbac3fe451756b6468258c78d558a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2 diff -r cb5691381acb -r 555971edd46e README.rst --- a/README.rst Thu Jun 08 17:36:38 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -# Wrapper of the variant caller 'MANTA', for use it as a Galaxy-based tool : - -Run the following commands in a terminal: - -planemo s - -Open in your browser: - -http://127.0.0.1:9090/ - diff -r cb5691381acb -r 555971edd46e candidateSV.vcf.gz Binary file candidateSV.vcf.gz has changed diff -r cb5691381acb -r 555971edd46e candidateSmallIndels.vcf.gz Binary file candidateSmallIndels.vcf.gz has changed diff -r cb5691381acb -r 555971edd46e manta.xml --- a/manta.xml Thu Jun 08 17:36:38 2023 +0000 +++ b/manta.xml Tue Feb 20 08:31:27 2024 +0000 @@ -1,4 +1,4 @@ - + Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. manta_macros.xml @@ -10,6 +10,9 @@ @pipefail@ @set_reference_fasta_filename@ #set run_dir = './MantaWorkflow' + configManta=\$(which configManta.py) && + PATH=\${configManta/"configManta.py"/}:\$PATH && + printenv && cp $__tool_directory__/configManta.py.ini configManta.py.ini && #if str( $bam_input.bam_input_selector ) == "not_tumor_bam": ln -s '$bam_input.normal_bam_file' normal.bam && @@ -26,7 +29,7 @@ #end if #if str( $set_configuration.set_configuration_switch ) == "Customized": rm ./configManta.py.ini && - python '$__tool_directory__/customConfigManta.py' + python2 '$__tool_directory__/customConfigManta.py' --minCandidateVariantSize '$set_configuration.minCandidateVariantSize' --rnaMinCandidateVariantSize '$set_configuration.rnaMinCandidateVariantSize' --minEdgeObservations '$set_configuration.minEdgeObservations' @@ -112,7 +115,6 @@ - - - config_file_check == True - + candidateSV_check == True @@ -139,7 +139,7 @@ - + @@ -148,10 +148,11 @@ + - + @@ -160,10 +161,11 @@ + - + @@ -172,10 +174,11 @@ + - + @@ -184,10 +187,11 @@ + - + @@ -196,6 +200,7 @@ + diff -r cb5691381acb -r 555971edd46e manta_macros.xml --- a/manta_macros.xml Thu Jun 08 17:36:38 2023 +0000 +++ b/manta_macros.xml Tue Feb 20 08:31:27 2024 +0000 @@ -1,17 +1,18 @@ 1.6 - 8 + 9 + 20.05 &1 || echo "Error running samtools faidx for Manta" >&2 && + ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && + samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 && #else: - #set $reference_fasta_filename = str( $reference_source.index.fields.path ) + #set $reference_fasta_filename = str( $reference_source.index.fields.path ) #end if ]]> @@ -28,8 +29,8 @@ + manta samtools - manta diff -r cb5691381acb -r 555971edd46e somaticSV.vcf.gz Binary file somaticSV.vcf.gz has changed diff -r cb5691381acb -r 555971edd46e test-data/candidateSV.vcf.gz Binary file test-data/candidateSV.vcf.gz has changed diff -r cb5691381acb -r 555971edd46e test-data/candidateSmallIndels.vcf.gz Binary file test-data/candidateSmallIndels.vcf.gz has changed diff -r cb5691381acb -r 555971edd46e test-data/conf_file_1.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conf_file_1.ini Tue Feb 20 08:31:27 2024 +0000 @@ -0,0 +1,58 @@ + +# +# This section contains all configuration settings for the top-level manta workflow, +# +[manta] + +referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa + +# Run discovery and candidate reporting for all SVs/indels at or above this size +# Separate option (to provide different default) used for runs in RNA-mode +minCandidateVariantSize = 8 +rnaMinCandidateVariantSize = 1000 + +# Remove all edges from the graph unless they're supported by this many 'observations'. +# Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted. +minEdgeObservations = 3 + +# If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge. +# Set to 0 to turn this filtration off +graphNodeMaxEdgeCount = 10 + +# Run discovery and candidate reporting for all SVs/indels with at least this +# many spanning support observations +minCandidateSpanningCount = 3 + +# After candidate identification, only score and report SVs/indels at or above this size: +minScoredVariantSize = 50 + +# minimum VCF "QUAL" score for a variant to be included in the diploid vcf: +minDiploidVariantScore = 10 + +# VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf: +minPassDiploidVariantScore = 20 + +# minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf: +minPassDiploidGTScore = 15 + +# somatic quality scores below this level are not included in the somatic vcf: +minSomaticScore = 10 + +# somatic quality scores below this level are filtered in the somatic vcf: +minPassSomaticScore = 30 + +# Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote +# locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads +# can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime +# burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read +# retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling. +# This feature can be enabled/disabled separately for germline and cancer calling below. +# +# Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes +# all other calling modes. +enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1 +enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0 + +# Set if an overlapping read pair will be considered as evidence +# Set to 0 to skip overlapping read pairs +useOverlapPairEvidence = 0 diff -r cb5691381acb -r 555971edd46e test-data/conf_file_2.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conf_file_2.ini Tue Feb 20 08:31:27 2024 +0000 @@ -0,0 +1,16 @@ +[manta] +referenceFasta = /dummy/path/to/genome.fa +enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1 +minPassSomaticScore = 30 +minSomaticScore = 10 +minCandidateVariantSize = 8 +minPassDiploidVariantScore = 20 +useOverlapPairEvidence = 0 +minPassDiploidGTScore = 15 +graphNodeMaxEdgeCount = 10 +minEdgeObservations = 3 +minDiploidVariantScore = 10 +minCandidateSpanningCount = 3 +enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0 +rnaMinCandidateVariantSize = 1000 +minScoredVariantSize = 50 diff -r cb5691381acb -r 555971edd46e test-data/conf_file_3.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conf_file_3.ini Tue Feb 20 08:31:27 2024 +0000 @@ -0,0 +1,58 @@ + +# +# This section contains all configuration settings for the top-level manta workflow, +# +[manta] + +referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa + +# Run discovery and candidate reporting for all SVs/indels at or above this size +# Separate option (to provide different default) used for runs in RNA-mode +minCandidateVariantSize = 8 +rnaMinCandidateVariantSize = 1000 + +# Remove all edges from the graph unless they're supported by this many 'observations'. +# Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted. +minEdgeObservations = 3 + +# If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge. +# Set to 0 to turn this filtration off +graphNodeMaxEdgeCount = 10 + +# Run discovery and candidate reporting for all SVs/indels with at least this +# many spanning support observations +minCandidateSpanningCount = 3 + +# After candidate identification, only score and report SVs/indels at or above this size: +minScoredVariantSize = 50 + +# minimum VCF "QUAL" score for a variant to be included in the diploid vcf: +minDiploidVariantScore = 10 + +# VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf: +minPassDiploidVariantScore = 20 + +# minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf: +minPassDiploidGTScore = 15 + +# somatic quality scores below this level are not included in the somatic vcf: +minSomaticScore = 10 + +# somatic quality scores below this level are filtered in the somatic vcf: +minPassSomaticScore = 30 + +# Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote +# locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads +# can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime +# burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read +# retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling. +# This feature can be enabled/disabled separately for germline and cancer calling below. +# +# Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes +# all other calling modes. +enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1 +enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0 + +# Set if an overlapping read pair will be considered as evidence +# Set to 0 to skip overlapping read pairs +useOverlapPairEvidence = 0 diff -r cb5691381acb -r 555971edd46e test-data/conf_file_4.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conf_file_4.ini Tue Feb 20 08:31:27 2024 +0000 @@ -0,0 +1,58 @@ + +# +# This section contains all configuration settings for the top-level manta workflow, +# +[manta] + +referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa + +# Run discovery and candidate reporting for all SVs/indels at or above this size +# Separate option (to provide different default) used for runs in RNA-mode +minCandidateVariantSize = 8 +rnaMinCandidateVariantSize = 1000 + +# Remove all edges from the graph unless they're supported by this many 'observations'. +# Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted. +minEdgeObservations = 3 + +# If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge. +# Set to 0 to turn this filtration off +graphNodeMaxEdgeCount = 10 + +# Run discovery and candidate reporting for all SVs/indels with at least this +# many spanning support observations +minCandidateSpanningCount = 3 + +# After candidate identification, only score and report SVs/indels at or above this size: +minScoredVariantSize = 50 + +# minimum VCF "QUAL" score for a variant to be included in the diploid vcf: +minDiploidVariantScore = 10 + +# VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf: +minPassDiploidVariantScore = 20 + +# minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf: +minPassDiploidGTScore = 15 + +# somatic quality scores below this level are not included in the somatic vcf: +minSomaticScore = 10 + +# somatic quality scores below this level are filtered in the somatic vcf: +minPassSomaticScore = 30 + +# Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote +# locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads +# can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime +# burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read +# retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling. +# This feature can be enabled/disabled separately for germline and cancer calling below. +# +# Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes +# all other calling modes. +enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1 +enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0 + +# Set if an overlapping read pair will be considered as evidence +# Set to 0 to skip overlapping read pairs +useOverlapPairEvidence = 0 diff -r cb5691381acb -r 555971edd46e test-data/conf_file_5.ini --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conf_file_5.ini Tue Feb 20 08:31:27 2024 +0000 @@ -0,0 +1,58 @@ + +# +# This section contains all configuration settings for the top-level manta workflow, +# +[manta] + +referenceFasta = /illumina/development/Isis/Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa + +# Run discovery and candidate reporting for all SVs/indels at or above this size +# Separate option (to provide different default) used for runs in RNA-mode +minCandidateVariantSize = 8 +rnaMinCandidateVariantSize = 1000 + +# Remove all edges from the graph unless they're supported by this many 'observations'. +# Note that one supporting read pair or split read usually equals one observation, but evidence is sometimes downweighted. +minEdgeObservations = 3 + +# If both nodes of an edge have an edge count higher than this, then skip evaluation of the edge. +# Set to 0 to turn this filtration off +graphNodeMaxEdgeCount = 10 + +# Run discovery and candidate reporting for all SVs/indels with at least this +# many spanning support observations +minCandidateSpanningCount = 3 + +# After candidate identification, only score and report SVs/indels at or above this size: +minScoredVariantSize = 50 + +# minimum VCF "QUAL" score for a variant to be included in the diploid vcf: +minDiploidVariantScore = 10 + +# VCF "QUAL" score below which a variant is marked as filtered in the diploid vcf: +minPassDiploidVariantScore = 20 + +# minimum genotype quality score below which single samples are filtered for a variant in the diploid vcf: +minPassDiploidGTScore = 15 + +# somatic quality scores below this level are not included in the somatic vcf: +minSomaticScore = 10 + +# somatic quality scores below this level are filtered in the somatic vcf: +minPassSomaticScore = 30 + +# Remote read retrieval is used ot improve the assembly of putative insertions by retrieving any mate reads in remote +# locations with poor mapping quality, which pair to confidently mapping reads near the insertion locus. These reads +# can help to fully assemble longer insertions, under certain circumstances this feature can add a very large runtime +# burden. For instance, given the very high chimeric pair rates found in degraded FFPE samples, the runtime of the read +# retrieval process can be unpredicable. For this reason the feature is disabled by default for somatic variant calling. +# This feature can be enabled/disabled separately for germline and cancer calling below. +# +# Here "CancerCallingModes" includes tumor-normal subtraction and tumor-only calling. "GermlineCallingModes" includes +# all other calling modes. +enableRemoteReadRetrievalForInsertionsInGermlineCallingModes = 1 +enableRemoteReadRetrievalForInsertionsInCancerCallingModes = 0 + +# Set if an overlapping read pair will be considered as evidence +# Set to 0 to skip overlapping read pairs +useOverlapPairEvidence = 0 diff -r cb5691381acb -r 555971edd46e test-data/somaticSV.vcf.gz Binary file test-data/somaticSV.vcf.gz has changed