v1.1.0

What's Changed

• workflow structure 1st push by @georgiesamaha in #1
• Svcallers by @georgiesamaha in #4
• fixed manta process- all sv callers done by @georgiesamaha in #6
• Variant calling processes complete by @georgiesamaha in #7
• clean .vscode by @georgiesamaha in #8
• v1.0 release by @georgiesamaha in #11
• backup, annotSV todo by @georgiesamaha in #12
• Betarelease by @georgiesamaha in #15
• fix typo by @SarahBeecroft in #25
• Added manta container, fixed some spacing by @SarahBeecroft in #21
• Create setonix.config by @SarahBeecroft in #22
• Create SLURM_setonix_runpipeline.sh by @SarahBeecroft in #23
• Add info about reference files by @SarahBeecroft in #24
• added setonix.config to this file by @SarahBeecroft in #28
• added gadi config by @georgiesamaha in #29
• remove dummy account variable by @SarahBeecroft in #31
• add newer tidbit container by @SarahBeecroft in #32
• include specific timings for jobs by @SarahBeecroft in #36
• run small jobs with local executor by @SarahBeecroft in #37
• run small jobs with small slurm allocation by @SarahBeecroft in #38
• Flexible AnnotSV annotation mode by @georgiesamaha in #39
• Apply additional flags to AnnotSV by @georgiesamaha in #40
• Create trace timestamp by @georgiesamaha in #41
• Flexible customisation options by @georgiesamaha in #42
• Add tower.yml and params.json for tower configurations by @georgiesamaha in #44
• remove tower.yml by @georgiesamaha in #45
• Tidy up parameters for tower integration by @georgiesamaha in #46
• Fix parameters for tower by @georgiesamaha in #47
• tower implementation fixes by @georgiesamaha in #48
• fix manta container, fix pbs script by @georgiesamaha in #49
• Fix indenting of nextflow.config by @georgiesamaha in #50
• Update nextflow_schema.json for tower by @georgiesamaha in #51
• Update nextflow_schema.json by @georgiesamaha in #52
• Fix gadi.config beforeScript by @georgiesamaha in #53
• Remove beforeScript by @georgiesamaha in #54
• Update gadi.config by @georgiesamaha in #55
• Tower Gadi implementation by @georgiesamaha in #56
• Add gdata to gadi config by @georgiesamaha in #58
• Gadi local jobs failing to access 10Gb memory by @georgiesamaha in #59
• Finalise Tower integration with scalable run on Gadi by @georgiesamaha in #61
• Fix issue #65: mix up of pbs and gadi parameters by @georgiesamaha in #66
• Fixed *.config & queue in PBS_gadi_runpipeline.sh by @chlu0571 in #67
• change nextflow.config & hashed beforeScript in gadi.config by @chlu0571 in #68
• Final release of workflow v1.0.0 by @georgiesamaha in #73

New Contributors

• @georgiesamaha made their first contribution in #1
• @SarahBeecroft made their first contribution in #25
• @chlu0571 made their first contribution in #67

Full Changelog: https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/commits/v1.1.0

v1.0.0

What's Changed

• workflow structure 1st push by @georgiesamaha in #1
• Svcallers by @georgiesamaha in #4
• fixed manta process- all sv callers done by @georgiesamaha in #6
• Variant calling processes complete by @georgiesamaha in #7
• clean .vscode by @georgiesamaha in #8
• v1.0 release by @georgiesamaha in #11
• backup, annotSV todo by @georgiesamaha in #12
• Betarelease by @georgiesamaha in #15
• fix typo by @SarahBeecroft in #25
• Added manta container, fixed some spacing by @SarahBeecroft in #21
• Create setonix.config by @SarahBeecroft in #22
• Create SLURM_setonix_runpipeline.sh by @SarahBeecroft in #23
• Add info about reference files by @SarahBeecroft in #24
• added setonix.config to this file by @SarahBeecroft in #28
• added gadi config by @georgiesamaha in #29
• remove dummy account variable by @SarahBeecroft in #31
• add newer tidbit container by @SarahBeecroft in #32
• include specific timings for jobs by @SarahBeecroft in #36
• run small jobs with local executor by @SarahBeecroft in #37
• run small jobs with small slurm allocation by @SarahBeecroft in #38
• Flexible AnnotSV annotation mode by @georgiesamaha in #39
• Apply additional flags to AnnotSV by @georgiesamaha in #40
• Create trace timestamp by @georgiesamaha in #41
• Flexible customisation options by @georgiesamaha in #42
• Add tower.yml and params.json for tower configurations by @georgiesamaha in #44
• remove tower.yml by @georgiesamaha in #45
• Tidy up parameters for tower integration by @georgiesamaha in #46
• Fix parameters for tower by @georgiesamaha in #47
• tower implementation fixes by @georgiesamaha in #48
• fix manta container, fix pbs script by @georgiesamaha in #49
• Fix indenting of nextflow.config by @georgiesamaha in #50
• Update nextflow_schema.json for tower by @georgiesamaha in #51
• Update nextflow_schema.json by @georgiesamaha in #52
• Fix gadi.config beforeScript by @georgiesamaha in #53
• Remove beforeScript by @georgiesamaha in #54
• Update gadi.config by @georgiesamaha in #55
• Tower Gadi implementation by @georgiesamaha in #56
• Add gdata to gadi config by @georgiesamaha in #58
• Gadi local jobs failing to access 10Gb memory by @georgiesamaha in #59
• Finalise Tower integration with scalable run on Gadi by @georgiesamaha in #61
• Fix issue #65: mix up of pbs and gadi parameters by @georgiesamaha in #66
• Fixed *.config & queue in PBS_gadi_runpipeline.sh by @chlu0571 in #67
• change nextflow.config & hashed beforeScript in gadi.config by @chlu0571 in #68
• Final release of workflow v1.0.0 by @georgiesamaha in #73

New Contributors

• @georgiesamaha made their first contribution in #1
• @SarahBeecroft made their first contribution in #25
• @chlu0571 made their first contribution in #67

Full Changelog: https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/commits/v1.0.0