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malariagen
/
pipelines
Pipelines for processing malaria parasite and mosquito genome sequence data.
MIT License
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import from irods using manifest with columns sample_id, irods_path
#67
tnguyensanger
closed
3 years ago
4
malaria-dk lsf group deprecated
#66
tnguyensanger
closed
2 years ago
0
Fix farm5 singularity to docker
#65
Lfulcrum
closed
3 years ago
0
Farm5 singularity to docker
#64
Lfulcrum
closed
3 years ago
0
setting bwa chunk size to 10M to achieve deterministic results
#63
magnusmanske
closed
3 years ago
0
Vector Read Backed Phasing
#62
jessicaway
closed
3 years ago
0
Align import workflows with changes in #51
#61
Lfulcrum
closed
3 years ago
2
Convert cram to bam in vector alignment pipeline
#60
tnguyensanger
closed
2 years ago
0
Moved static files (references and allele sites) to a production loca…
#59
seretol
closed
3 years ago
0
Release a single file containing wdl, options and dependencies to sim…
#58
seretol
closed
3 years ago
0
Release on tag
#57
seretol
closed
3 years ago
0
Cromwell configurations on farm5 are using localization = copy, which explodes size of workflow working directory
#56
tnguyensanger
closed
2 years ago
0
Concordance calculations for vector genotype
#55
seretol
closed
3 years ago
1
Determine final lanelet manifest fields required for vector alignment and genotyping
#54
tnguyensanger
closed
2 years ago
1
Create pipeline to Import batch of samples from IRODS and run each sample through alignment and genotyping
#53
tnguyensanger
closed
3 years ago
0
Create pipelines that download multiple samples from IRODS in a batch
#52
tnguyensanger
closed
2 years ago
0
Performance improvements / Operations improvements
#51
gbggrant
closed
3 years ago
1
Script to select variants and recode alleles for phasing
#50
alimanfoo
closed
3 years ago
3
Vector genotype concordance calculations + tests
#49
seretol
closed
3 years ago
1
Output VCF Index
#48
gbggrant
closed
4 years ago
0
Update RunningAPipeline.md
#47
tnguyensanger
closed
4 years ago
1
Update RunningAPipeline.md
#46
tnguyensanger
closed
3 years ago
0
Genotype Concordance Validation of genotyping pipelines
#45
tnguyensanger
closed
2 years ago
10
Mosquito phasing pipeline development
#44
alimanfoo
closed
2 years ago
22
Add SNP Genotyping pipeline, changes to ShortReadAlignment, etc.
#43
gbggrant
closed
4 years ago
0
Add lanelets for SNP calling validation
#42
alimanfoo
closed
4 years ago
0
How to make bwa short read alignment deterministic for testing
#41
tnguyensanger
closed
2 years ago
1
Added Dockerfile and single-task WDL for baseline amplicon SNP calling parasite pipeline.
#40
samuelklee
closed
4 years ago
7
Add support for cram, bam, and fastq inputs to the ShortReadAlignment.wd
#39
gbggrant
closed
4 years ago
3
Add platform argument to build_pipeline_release script
#38
gbggrant
closed
2 years ago
2
Port baseline Plasmodium amplicon SNP calling pipeline.
#37
samuelklee
closed
4 years ago
1
vcf_to_zarr script
#36
tnguyensanger
closed
4 years ago
9
Copy script to convert vcf to zarr to this repo
#35
tnguyensanger
closed
4 years ago
0
Test PR for WDL validation github action
#34
jessicaway
closed
4 years ago
0
Validation/truth datasets for variant calling calibration, comparison and evaluation
#33
alimanfoo
closed
2 years ago
26
Input source for mosquito short read alignment pipeline
#32
alimanfoo
closed
2 years ago
3
Revise structure of pipelines
#31
gbggrant
closed
4 years ago
0
Changes for clarity following BI queries
#30
hardingnj
closed
4 years ago
1
Adding GitHub Action to Validate WDL files.
#29
gbggrant
closed
4 years ago
0
Minimal input crams
#28
tnguyensanger
closed
4 years ago
0
Define read group contents in vector short read alignment pipelines
#27
tnguyensanger
closed
2 years ago
1
Provide example crams released by Core Sequencing
#26
tnguyensanger
closed
2 years ago
3
Minimal input to validate plumbing of vector short read pipelines
#25
tnguyensanger
closed
2 years ago
5
Short Read Alignment Pipeline Farm5 implementation
#24
gbggrant
closed
4 years ago
0
Fix error in short read alignment pipeline fixture
#23
alimanfoo
closed
4 years ago
0
Mosquito short read alignment pipeline - validation
#22
alimanfoo
closed
2 years ago
13
Vector phasing pipeline spec
#21
alimanfoo
closed
4 years ago
3
Vector SNP genotyping spec
#20
alimanfoo
closed
4 years ago
3
Add IRODS inputs for vector short read alignment pipeline
#19
alimanfoo
closed
4 years ago
0
Update vector Short Read Alignment Spec and WDL for removal of calmd
#18
gbggrant
closed
4 years ago
0
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