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malariagen
/
pipelines
Pipelines for processing malaria parasite and mosquito genome sequence data.
MIT License
14
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13
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Add max retries runtime attribute
#117
ahernank
closed
6 months ago
0
Vector CNV pipeline version 1.0.0
#116
jessicaway
closed
6 months ago
0
Bump numpy from 1.19.1 to 1.22.0 in /dockerfiles/SampleSelectVariants
#115
dependabot[bot]
opened
1 year ago
0
Add CNVcoverage and TargetRegions sub-pipelines
#114
jessicaway
closed
6 months ago
0
Updating feature branch with the latest master branch.
#113
kevinpalis
closed
1 year ago
0
Add cnv vector spec
#112
jessicaway
closed
1 year ago
0
WIP CNV pipeline dev
#111
alimanfoo
closed
6 months ago
0
Increased memory for 'select variants'
#110
jorels1
closed
1 year ago
0
Number of SNPs and Indels doesn't match with the numbers reported in README files
#109
Rohit-Satyam
closed
1 year ago
4
Increase disk for read alignment (bwa mem)
#108
alimanfoo
closed
1 year ago
0
More resource limit tweaks for short read alignment
#107
alimanfoo
closed
1 year ago
0
Resource limit tweaks to alignment tasks
#106
alimanfoo
closed
1 year ago
0
Bump numpy from 1.19.1 to 1.22.0 in /dockerfiles/CohortVcfToZarr
#105
dependabot[bot]
opened
2 years ago
0
Bump numpy from 1.19.1 to 1.22.0 in /scripts/sample_select_variants
#104
dependabot[bot]
opened
2 years ago
0
Bump numpy from 1.19.1 to 1.21.0 in /dockerfiles/SampleSelectVariants
#103
dependabot[bot]
closed
1 year ago
1
Bump numpy from 1.19.1 to 1.21.0 in /scripts/sample_select_variants
#102
dependabot[bot]
closed
2 years ago
1
Bump numpy from 1.19.1 to 1.21.0 in /dockerfiles/CohortVcfToZarr
#101
dependabot[bot]
closed
2 years ago
1
Optimise GCP VcfToZarr and generalise to handle other vector species with different contigs
#100
alimanfoo
closed
2 years ago
6
Add disk size to ShapeIt4 when using a reference panel
#99
jessicaway
closed
2 years ago
0
increased memory
#98
SimonSuddaby
closed
2 years ago
0
Add zones to task runtime for Phasing pipeline
#97
jessicaway
closed
2 years ago
0
remove ref from cram decode (farm5)
#96
Oliver-Lorenz-dev
closed
2 years ago
2
update docker image tag
#95
GvandeSteeg
closed
2 years ago
0
Update sample_vcf_to_zarr.py
#94
GvandeSteeg
closed
2 years ago
10
Support phasing with a reference panel
#93
jessicaway
closed
3 years ago
0
Update ShapeIt4 from version 4.1.3 to version 4.2.1
#92
jessicaway
closed
3 years ago
0
Adding CNV scripts
#91
EricRLucas
opened
3 years ago
0
Additional resources for statistical phasing
#90
jessicaway
closed
3 years ago
0
More memory for ReadBackedPhasing
#89
jessicaway
closed
3 years ago
0
Additional resources for large phasing set
#88
jessicaway
closed
3 years ago
0
Add post-pipeline check scripts and README
#87
Lfulcrum
opened
3 years ago
0
Parallelize ShapeIt4 over genome regions
#86
jessicaway
closed
3 years ago
0
Phasing benchmarking
#85
jessicaway
closed
3 years ago
0
Publish dockstore workflows
#84
jessicaway
closed
3 years ago
0
Add dockstore yml file
#83
jessicaway
closed
3 years ago
0
Modify cohort_vcf_to_zarr.py to optionally output a zipped zarr.
#82
gbggrant
closed
3 years ago
1
Ported phasing pipeline from GCP to Farm5
#81
gbggrant
closed
3 years ago
0
Ag3.0 phasing pipeline production run
#80
alimanfoo
closed
2 years ago
15
Update gcp version of SNPGenotypingTasks.wdl
#79
gbggrant
closed
3 years ago
0
Change SNPGenotyping to compress vcf and create tabix index
#78
Lfulcrum
closed
3 years ago
0
Update dockerfiles
#77
Lfulcrum
closed
3 years ago
0
Updating gcp flavor of Vector pipelines to handle updates applied to farm5
#76
gbggrant
closed
3 years ago
0
Add throttle_irods runtime attribute
#75
Lfulcrum
closed
3 years ago
0
Jw vector statistical phasing
#74
gbggrant
closed
3 years ago
1
Validate results for phasing pipeline
#73
hardingnj
closed
3 years ago
17
Cohort VCF to Zarr
#72
alimanfoo
closed
3 years ago
3
Allow for flexible columns in manifest for vector alignment genotyping pipeline
#71
tnguyensanger
opened
3 years ago
3
Use flexible fields in manifest
#70
tnguyensanger
closed
2 years ago
0
Migrating all data to gs://malariagen bucket
#69
gbggrant
closed
3 years ago
0
Output of vector short read alignment pipeline is named *.bam.bam
#68
tnguyensanger
closed
2 years ago
1
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