sydney-informatics-hub/germline-structuralv-nf issues and pull requests

#76 - Remove harcoded `GRCh38` version for `AnnotSv`

Pull Request - State: closed - Opened by juanesarango about 2 months ago - 1 comment

#76 - Remove harcoded `GRCh38` version for `AnnotSv`

Pull Request - State: closed - Opened by juanesarango about 2 months ago - 1 comment

#75 - Add Picard ValidateSamFile module

Issue - State: open - Opened by calizilla 11 months ago
Labels: enhancement

#75 - Add Picard ValidateSamFile module

Issue - State: open - Opened by calizilla 11 months ago
Labels: enhancement

#74 - Final release

Issue - State: closed - Opened by georgiesamaha 11 months ago

#74 - Final release

Issue - State: closed - Opened by georgiesamaha 11 months ago

#73 - Final release of workflow v1.0.0

Pull Request - State: closed - Opened by georgiesamaha 11 months ago

#73 - Final release of workflow v1.0.0

Pull Request - State: closed - Opened by georgiesamaha 11 months ago

#72 - Feature request: check bam index age or presence and reindex if needed

Issue - State: open - Opened by georgiesamaha 12 months ago
Labels: enhancement

#72 - Feature request: check bam index age or presence and reindex if needed

Issue - State: open - Opened by georgiesamaha 12 months ago
Labels: enhancement

#71 - Read samplesheet via column position not header label

Issue - State: open - Opened by calizilla 12 months ago

#71 - Read samplesheet via column position not header label

Issue - State: open - Opened by calizilla 12 months ago

#70 - Add additional checks to check_cohort.nf

Issue - State: open - Opened by calizilla 12 months ago
Labels: enhancement

#70 - Add additional checks to check_cohort.nf

Issue - State: open - Opened by calizilla 12 months ago
Labels: enhancement

#69 - Reference fasta is staged by tiddit module but not used

Issue - State: open - Opened by calizilla 12 months ago

#69 - Reference fasta is staged by tiddit module but not used

Issue - State: open - Opened by calizilla 12 months ago

#68 - change nextflow.config & hashed beforeScript in gadi.config

Pull Request - State: closed - Opened by chlu0571 12 months ago

#68 - change nextflow.config & hashed beforeScript in gadi.config

Pull Request - State: closed - Opened by chlu0571 12 months ago

#67 - Fixed *.config & queue in PBS_gadi_runpipeline.sh

Pull Request - State: closed - Opened by chlu0571 12 months ago

#67 - Fixed *.config & queue in PBS_gadi_runpipeline.sh

Pull Request - State: closed - Opened by chlu0571 12 months ago

#66 - Fix issue #65: mix up of pbs and gadi parameters

Pull Request - State: closed - Opened by georgiesamaha 12 months ago

#66 - Fix issue #65: mix up of pbs and gadi parameters

Pull Request - State: closed - Opened by georgiesamaha 12 months ago

#65 - Inconsistent parameter definition and application for gadi account

Issue - State: closed - Opened by georgiesamaha about 1 year ago - 1 comment
Labels: bug

#65 - Inconsistent parameter definition and application for gadi account

Issue - State: closed - Opened by georgiesamaha about 1 year ago - 1 comment
Labels: bug

#64 - pullContainers.sh not utilising specified cachedir

Issue - State: closed - Opened by calizilla about 1 year ago - 2 comments

#64 - pullContainers.sh not utilising specified cachedir

Issue - State: closed - Opened by calizilla about 1 year ago - 2 comments

#63 - Pre-download images

Issue - State: closed - Opened by calizilla about 1 year ago - 2 comments

#62 - Add KSU usage estimates for resource management

Issue - State: closed - Opened by calizilla about 1 year ago
Labels: enhancement

#62 - Add KSU usage estimates for resource management

Issue - State: closed - Opened by calizilla about 1 year ago
Labels: enhancement

#61 - Finalise Tower integration with scalable run on Gadi

Pull Request - State: closed - Opened by georgiesamaha about 1 year ago

#61 - Finalise Tower integration with scalable run on Gadi

Pull Request - State: closed - Opened by georgiesamaha about 1 year ago

#60 - Tower integration

Issue - State: closed - Opened by georgiesamaha about 1 year ago - 2 comments

#59 - Gadi local jobs failing to access 10Gb memory

Pull Request - State: closed - Opened by georgiesamaha about 1 year ago

#58 - Add gdata to gadi config

Pull Request - State: closed - Opened by georgiesamaha about 1 year ago

#57 - Add Tower.yaml for report exposure on interface

Issue - State: closed - Opened by georgiesamaha about 1 year ago - 2 comments

#56 - Tower Gadi implementation

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#55 - Update gadi.config

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#54 - Remove beforeScript

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#53 - Fix gadi.config beforeScript

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#52 - Update nextflow_schema.json

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#51 - Update nextflow_schema.json for tower

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#50 - Fix indenting of nextflow.config

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#49 - fix manta container, fix pbs script

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#48 - tower implementation fixes

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#47 - Fix parameters for tower

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#46 - Tidy up parameters for tower integration

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#45 - remove tower.yml

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#44 - Add tower.yml and params.json for tower configurations

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#43 - nextflow_schema.json

Issue - State: closed - Opened by georgiesamaha over 1 year ago

#42 - Flexible customisation options

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#41 - Create trace timestamp

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#40 - Apply additional flags to AnnotSV

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#39 - Flexible AnnotSV annotation mode

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago
Labels: enhancement

#38 - run small jobs with small slurm allocation

Pull Request - State: closed - Opened by SarahBeecroft over 1 year ago

#37 - run small jobs with local executor

Pull Request - State: closed - Opened by SarahBeecroft over 1 year ago

#36 - include specific timings for jobs

Pull Request - State: closed - Opened by SarahBeecroft over 1 year ago

#35 - Add CNV module

Issue - State: closed - Opened by georgiesamaha over 1 year ago - 1 comment
Labels: enhancement

#34 - Annotation type flag for AnnotSV

Issue - State: closed - Opened by georgiesamaha over 1 year ago
Labels: enhancement

#33 - -SVminSize flag for AnnotSV

Issue - State: closed - Opened by georgiesamaha over 1 year ago

#32 - add newer tidbit container

Pull Request - State: closed - Opened by SarahBeecroft over 1 year ago

#31 - remove dummy account variable

Pull Request - State: closed - Opened by SarahBeecroft over 1 year ago

#30 - Pipeline feedback

Issue - State: closed - Opened by gavinmonahan over 1 year ago - 5 comments

#29 - added gadi config

Pull Request - State: closed - Opened by georgiesamaha over 1 year ago

#28 - added setonix.config to this file

Pull Request - State: closed - Opened by SarahBeecroft almost 2 years ago

#27 - Portability testing @ Pawsey Setonix

Issue - State: closed - Opened by georgiesamaha almost 2 years ago

#26 - Run scripts for Setonix and Gadi

Issue - State: closed - Opened by georgiesamaha almost 2 years ago
Labels: enhancement

#25 - fix typo

Pull Request - State: closed - Opened by SarahBeecroft almost 2 years ago

#24 - Add info about reference files

Pull Request - State: closed - Opened by SarahBeecroft almost 2 years ago

#23 - Create SLURM_setonix_runpipeline.sh

Pull Request - State: closed - Opened by SarahBeecroft almost 2 years ago - 1 comment

#22 - Create setonix.config

Pull Request - State: closed - Opened by SarahBeecroft almost 2 years ago

#21 - Added manta container, fixed some spacing

Pull Request - State: closed - Opened by SarahBeecroft almost 2 years ago

#20 - Bug in Tiddit when using alt-contigs

Issue - State: closed - Opened by SarahBeecroft almost 2 years ago - 2 comments

#19 - CITATION file

Issue - State: closed - Opened by georgiesamaha almost 2 years ago

#18 - Explore variant prioritisation features

Issue - State: closed - Opened by georgiesamaha almost 2 years ago - 1 comment

#17 - Add infrastructure-specific configs

Issue - State: closed - Opened by georgiesamaha almost 2 years ago - 2 comments

#16 - Merging stringency evaluation

Issue - State: closed - Opened by georgiesamaha almost 2 years ago

#15 - Betarelease

Pull Request - State: closed - Opened by georgiesamaha almost 2 years ago

#14 - Optional AnnotSV integration (human/mouse only)

Issue - State: closed - Opened by georgiesamaha almost 2 years ago - 1 comment
Labels: enhancement

#13 - Test with use case dataset (PIPE-2988)

Issue - State: closed - Opened by georgiesamaha almost 2 years ago

#12 - backup, annotSV todo

Pull Request - State: closed - Opened by georgiesamaha almost 2 years ago

#11 - v1.0 release

Pull Request - State: closed - Opened by georgiesamaha about 2 years ago

#10 - VEP annotation troubleshooting

Issue - State: closed - Opened by georgiesamaha about 2 years ago - 3 comments
Labels: enhancement, wontfix

#9 - SURVIVOR merging of vcfs with nextflow

Issue - State: closed - Opened by georgiesamaha about 2 years ago

#8 - clean .vscode

Pull Request - State: closed - Opened by georgiesamaha about 2 years ago

#7 - Variant calling processes complete

Pull Request - State: closed - Opened by georgiesamaha about 2 years ago

#6 - fixed manta process- all sv callers done

Pull Request - State: closed - Opened by georgiesamaha about 2 years ago

#5 - Revert "Svcallers"

Pull Request - State: closed - Opened by georgiesamaha about 2 years ago

#4 - Svcallers

Pull Request - State: closed - Opened by georgiesamaha about 2 years ago
Labels: enhancement

#3 - Build individual SV subworkflows as modules

Issue - State: closed - Opened by georgiesamaha about 2 years ago

#2 - Manta process --callRegions specification

Issue - State: closed - Opened by georgiesamaha about 2 years ago
Labels: enhancement

#1 - workflow structure 1st push

Pull Request - State: closed - Opened by georgiesamaha about 2 years ago

GitHub / sydney-informatics-hub/germline-structuralv-nf issues and pull requests