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lightning.git
2024-04-11
Peter Amstutz
Make the inputs optional instead of "default: null...
20461-updating-gvcf-pa
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2023-09-20
Alex Coleman
20461 Updating README
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2023-09-14
Alex Coleman
20461: Updating main workflow and README.md
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2023-08-22
Alex Coleman
20461 updating resource requirements
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2023-08-22
Alex Coleman
20461: Updating workflow and README.
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2023-07-31
Alex Coleman
20461: Updating to support multiple possible types...
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2023-07-20
Alex Coleman
Adding copyright headers.
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2023-07-20
Alex Coleman
Updating README.md to further explain different inputs.
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2023-07-20
Alex Coleman
Updating README to better describe what inputs are...
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2023-07-20
acoleman2000
Updating main workflow for appropriate conditional...
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2023-07-20
acoleman2000
Updating main workflow to add spacing.
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2023-07-20
acoleman2000
Updating workflow so scatter that occurs before conditi...
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2023-07-20
acoleman2000
Updating Dockerfile for vcfutil to point to my gvcf...
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2023-07-14
acoleman2000
Updating README.md.
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2023-07-14
acoleman2000
Removing files (moved to subdirs) and updating main wf.
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2023-07-14
acoleman2000
Organizing cwl files and creating conditional workflow.
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2023-07-14
acoleman2000
Adding README.md.
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2023-03-07
Tom Clegg
Merge branch '19995-glm-freq-threshold'
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2023-03-06
Tom Clegg
19995: Skip GLM on variants below frequency threshold.
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2023-02-02
Tom Clegg
Merge branch '19997-glm'
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2023-02-02
Tom Clegg
Preserve pca components from input when writing samples...
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2023-02-02
Tom Clegg
Fix validation=0 in samples.csv (should be empty for...
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2023-02-02
Tom Clegg
Turn off auto-retry.
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2023-01-27
Jiayong Li
Merge branch '19868-pca-in-ml' into main
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2023-01-27
Jiayong Li
Merge branch 'main' into 19868-pca-in-ml
19868-pca-in-ml
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2023-01-27
Jiayong Li
Change resource requirement of gvcf2fasta and imputation
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2023-01-20
Tom Clegg
Darker colors.
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2023-01-20
Tom Clegg
Bring back genomewideline/suggestiveline options.
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2023-01-20
Jiayong Li
Merge branch '19868-pca-in-ml' into main
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2023-01-20
Jiayong Li
Merge branch 'main' into 19868-pca-in-ml
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2023-01-20
Jiayong Li
Change slice-numpy-onehot parameter
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2023-01-19
Tom Clegg
Generate a manhattan plot for each chromosome.
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2023-01-13
Tom Clegg
Fix GLM p-value calculation when -case-control-only...
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2023-01-12
Jiayong Li
Merge branch '19868-pca-in-ml' into main
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2023-01-12
Jiayong Li
Merge branch 'main' into 19868-pca-in-ml
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2023-01-12
Jiayong Li
Fix shebang and license
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2023-01-10
Tom Clegg
Fix -min-coverage calculation broken when -case-control...
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2023-01-03
Tom Clegg
Add column headings to slice-numpy -pca sample list...
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2023-01-03
Tom Clegg
Fix validation flag in slice-numpy -pca sample list...
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2022-12-21
Tom Clegg
Merge branch '19526-manhattan-plot'
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2022-12-19
Tom Clegg
19526: Output tile locations and pvalues at specified...
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2022-12-19
Tom Clegg
Merge branch '19566-glm'
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2022-12-19
Tom Clegg
19566: Preemptible flag.
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2022-12-19
Tom Clegg
19566: Record number of p-value calculations performed.
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2022-12-16
Tom Clegg
19566: Silence logging from glm library.
19566-glm
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2022-12-16
Tom Clegg
19566: Fix chi2 used instead of logistic regression...
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2022-12-15
Jiayong Li
Merge branch '19785-add-cwl' into main
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2022-12-15
Jiayong Li
Merge branch 'main' into 19785-add-cwl
19785-add-cwl
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2022-12-15
Jiayong Li
Change lightning docker file so that it builds the...
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2022-12-15
Tom Clegg
19566: Merge branch 'main'
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2022-12-15
Tom Clegg
Merge branch '19526-manhattan-plot'
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2022-12-14
Tom Clegg
19566: Precompute cov glm.
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2022-12-13
Tom Clegg
Merge branch '19566-glm'
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2022-12-12
Tom Clegg
19566: Test p-value vs. Python.
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2022-12-12
Tom Clegg
19566: Normalize pca values before glm.
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2022-12-12
Tom Clegg
19566: Add constant, check GLM results against Python.
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2022-12-09
Jiayong Li
Merge branch '19785-add-cwl' into main
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2022-12-09
Jiayong Li
Fix readme
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2022-12-09
Jiayong Li
Merge branch '19785-add-cwl' into main
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2022-12-09
Jiayong Li
Add cwl and docker files
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2022-12-01
Tom Clegg
19526: Tidy manhattan plot.
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2022-11-29
Tom Clegg
19566: Option to limit pca components used in glm....
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2022-11-29
Tom Clegg
19566: glm one column at a time.
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2022-11-29
Tom Clegg
19566: Logistic regression p-value.
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2022-11-28
Tom Clegg
Merge branch '19526-manhattan-plot'
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2022-11-28
Tom Clegg
19526: Add manhattan plot.
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2022-11-18
Tom Clegg
Check for unparsed command line args.
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2022-11-18
Tom Clegg
19780: Fix indexing error.
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2022-11-16
Tom Clegg
19527: slice-numpy accepts samples.csv with or without...
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2022-11-16
Tom Clegg
19527: Update arvados sdk.
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2022-11-16
Tom Clegg
19527: Fix odd # columns to pca.
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2022-11-16
Tom Clegg
19527: Fix one-hot matrix.
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2022-11-16
Tom Clegg
19527: Enable choose-samples to work without case/contr...
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2022-11-16
Tom Clegg
19527: Fix Χ² calculation.
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2022-11-16
Tom Clegg
19527: Output samples.csv earlier.
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2022-11-16
Tom Clegg
19527: Fix crash on tag skipped for min-coverage.
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2022-11-16
Tom Clegg
19527: Option to exclude non-case/control samples.
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2022-11-10
Tom Clegg
Merge branch '19527-training-set'
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2022-11-09
Tom Clegg
19527: Accommodate header row in samples csv.
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2022-11-09
Tom Clegg
19527: Ignore empty line at EOF.
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2022-11-09
Tom Clegg
Merge branch '19524-pca'
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2022-11-09
Tom Clegg
19527: Fix p-value calculation.
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2022-11-09
Tom Clegg
19527: Load training-set flag from samples.csv.
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2022-11-09
Tom Clegg
19527: choose-samples: training/validation set.
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2022-11-09
Tom Clegg
19527: Load training-set flag from samples.csv.
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2022-11-07
Tom Clegg
choose-samples: training/validation set.
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2022-11-02
Tom Clegg
19524: Fit PCA to specified training set.
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2022-10-31
Tom Clegg
Merge branch '19524-pca'
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2022-10-21
Tom Clegg
19524: Fix matrix alloc size.
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2022-10-20
Tom Clegg
19524: Flags choose which PCA components to plot.
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2022-10-20
Tom Clegg
19524: Update colors, plot unknown-phenotype behind...
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2022-10-20
Tom Clegg
19524: Limit size of PCA input matrix.
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2022-10-19
Tom Clegg
19524: Limit size of PCA input matrix.
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2022-10-19
Tom Clegg
19524: configurable vcpus/ram
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2022-10-14
Tom Clegg
Merge branch '19524-pca'
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2022-10-14
Tom Clegg
19524: Use marker shape to indicate second category...
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2022-10-14
Tom Clegg
19524: Remove obsolete pca cmds.
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2022-10-14
Tom Clegg
19524: Fix deprecated scipy.load.
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2022-10-14
Tom Clegg
19524: Read multiple phenotype files.
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2022-10-14
Tom Clegg
19524: Generalize plot colors a little.
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