Separate modules #209
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Separate modules #209
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…dDataDir/preprocess
mumichae
reviewed
Jun 16, 2021
mumichae
reviewed
Jun 16, 2021
mumichae
reviewed
Jun 16, 2021
mumichae
reviewed
Jun 16, 2021
mumichae
reviewed
Jun 16, 2021
mumichae
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Jun 16, 2021
mumichae
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Jun 16, 2021
mumichae
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Jun 16, 2021
…into separate_modules
nickhsmith
commented
Jun 30, 2021
drop/template/Snakefile
Outdated
| include: drop.utils.getWBuildSnakefile() | ||
| include: cfg.AE.getWorkdir() + "/Snakefile" | ||
| include: cfg.AS.getWorkdir() + "/Snakefile" | ||
| include: cfg.MAE.getWorkdir() + "/Snakefile" | ||
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| # don't allow the dataset wildcard to contain '--' as this is a delimter |
vyepez88
approved these changes
Jun 30, 2021
Merged
c-mertes
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Jul 21, 2021
Major changes included in this update is: * adapt to new snakemake version (#208) * Speedup CI (use micromamba, #218) * Add HTML cutoff for results (#217) * Separate modules (#209) * Update documentation (#228) On top of this many small bug-fixes are included: * #175 #192 #198 #231 * Simplify result reporting Co-authored-by: Vicente Yepez <30469316+vyepez88@users.noreply.github.com> Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Michaela Mueller <51025211+mumichae@users.noreply.github.com> Co-authored-by: Michaela Mueller <mumichae@in.tum.de> Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: nickhsmith <smithnickh@gmail.com> Co-authored-by: Christian Mertes <mertes@in.tum.de>
nickhsmith
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Aug 11, 2021
* Update to version 1.1.0 (#229) Major changes included in this update is: * adapt to new snakemake version (#208) * Speedup CI (use micromamba, #218) * Add HTML cutoff for results (#217) * Separate modules (#209) * Update documentation (#228) On top of this many small bug-fixes are included: * #175 #192 #198 #231 * Simplify result reporting Co-authored-by: Vicente Yepez <30469316+vyepez88@users.noreply.github.com> Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Michaela Mueller <51025211+mumichae@users.noreply.github.com> Co-authored-by: Michaela Mueller <mumichae@in.tum.de> Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: nickhsmith <smithnickh@gmail.com> Co-authored-by: Christian Mertes <mertes@in.tum.de> * add splitting to MAE filterSNVs.sh * fix broken link and maxVarFreqCohort * fix broken link and maxVarFreqCohort * Update test_MAE.py * code review fixes Co-authored-by: Michaela Mueller <51025211+mumichae@users.noreply.github.com> Co-authored-by: Vicente Yepez <30469316+vyepez88@users.noreply.github.com> Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Michaela Mueller <mumichae@in.tum.de> Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de>
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Separate modules using config file options.
update submodule to have workDir attributes
update cli to correctly update drop from base dir
update Snakefile handling and shared input/output generation
method to ignore modules in wBuild by changing the filename to an ignorable path