This describes the different release versions of SNVPhyl.
Released on June 6, 2019.
- Docker -
phacnml/snvphyl-galaxy-1.1.0
- Galaxy Tools - suite_snvphyl_1_1_0
- Galaxy Workflows
- Paired-end: SNVPhyl Paired-End 1.1.0 and SNVPhyl Paired-End 1.1.0 (invalid-positions)
- Single-end: SNVPhyl Single-End 1.1.0 and SNVPhyl Single-End 1.1.0 (invalid-positions)
- Git - https://github.com/phac-nml/snvphyl-galaxy/tree/1.1.0
- Convert all SNVPhyl wrappers from tool shed package to bioconda (v1.8.2)
- Removed following unused/deprecated wrappers & capsules
- Wombac
- Seqtk NML
- package_perl_5_18_iuc
- package_msa_datatypes_iuc
- package_mummer_3_23
- bcf_bgzip
- Removed following wrappers that are now available on main public tool shed
- smalt
- freebayes
- bcftools mpileup
- phyml
- bcftools view
- bcftools call
- Enable CI testing with Travis
Released on January 23, 2017.
- Docker -
phacnml/snvphyl-galaxy-1.0.1
- Virtual Machine - snvphyl-galaxy-1.0.1.zip
- Galaxy Tools - suite_snvphyl_1_0_1
- Galaxy Workflows
- Paired-end: SNVPhyl Paired-End 1.0.1 and SNVPhyl Paired-End 1.0.1 (invalid-positions)
- Single-end: SNVPhyl Single-End 1.0.1 and SNVPhyl Single-End 1.0.1 (invalid-positions)
- Git - https://github.com/phac-nml/snvphyl-galaxy/tree/1.0.1
- Re-named parameter alternative-allele-ratio to snv-abundance-ratio.
- Added tool
positions2snv_alignment
to Galaxy to generate an alignment of only variant-containing positions. - Added tool
positions2snv_invariant_alignment
to Galaxy to generate an alignment of all (variant or non-variant) positions. - Updated density window size parameter to a default value of 500.
- Updated download location of dependency
package_zlib_1_2_8
. - Formatting/text changes to some Galaxy tools.
Released on May 25, 2016.
- Docker -
phacnml/snvphyl-galaxy-1.0
- Virtual Machine - snvphyl-galaxy-1.0.zip
- Galaxy Tools - suite_snvphyl_1_0_0
- Galaxy Workflows
- Paired-end: SNVPhyl Paired-End 1.0 and SNVPhyl Paired-End 1.0 (invalid-positions)
- Single-end: SNVPhyl Single-End 1.0 and SNVPhyl Single-End 1.0 (invalid-positions)
- Git - https://github.com/phac-nml/snvphyl-galaxy/tree/v1.0
- Additions
- Added ability to remove high-density SNV regions by adjusting a window size and threshold of SNVs.
- Added additional information to the
vcf2core.tsv
output file. - Added workflows for single-end sequence read data.
- Re-named many internal scripts to use terminology of SNV alignment instead of pseudoalignment.
- Fixes
- Fixed output of
filterStats.txt
to include invalid positions. - Additional checks to verify depth of coverage for invariant sites.
- Fixed behaviour of of tools like bcftools to enable re-scheduling within a cluster when run through Galaxy by ignoring existing output file.
- Fixed up issues with incorrect/missing dependencies among tools in Galaxy.
- Fixed output of
Released on November 13, 2015.
- Docker -
phacnml/snvphyl-galaxy-0.3
- Virtual Machine - snvphyl-galaxy-0.3.zip
- Galaxy Tools - suite_snvphyl_0_3_0
- Galaxy Workflow - SNVPhyl Paired-End 0.3 and SNVPhyl Paired-End 0.3 (invalid-positions)
- Git - https://irida.corefacility.ca/analysis-pipelines/snvphyl-galaxy/tree/v0.3
- Updated git URLs to reference new gitlab https://irida.corefacility.ca/analysis-pipelines/snvphyl-galaxy.
- Updated FreeBayes to refer to latest version in Galaxy freebayes_0_9_20_b040236
- Updated
samtools sort
to use multiple threads. - Made Do not perform INDEL calling the default for SAMtools mpileup.
Released on September 21, 2015.
- Docker -
phacnml/snvphyl-galaxy-0.2-beta-1
- Virtual Machine - snvphyl-galaxy-0.2-beta-1.zip
- Galaxy Tools - suite_snvphyl_0_2_0
- Galaxy Workflow - SNVPhyl Paired-End 0.2 and SNVPhyl Paired-End 0.2 (invalid-positions)
- Git - https://irida.corefacility.ca/analysis-pipelines/snvphyl-galaxy/tree/v0.2-beta-1
- Initial release of SNVPhyl run through Galaxy
- Includes Docker and Virtual Machine images
- Mapping/variant calling, variant merging, constructing phylogeny
- Quality checking tools for coverage, % of core used, and variants filtered