lrp_3.0.75

Add bumpversion cfg (#403)

• add .bumpversion.cfg

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Co-authored-by: bshifaw [email protected]

lrp_3.0.74

Update task descriptions (#402)

• updated description to wdl files in task Alignment, Assembly, and Preprocessing

• updated description to wdl files in task Transcriptomics

• updated description to wdl files in task QC

• updated description to wdl files in task Utility

• updated description to wdl files in task VariantCalling

• fixes to pass miniwdl validation

• fixes to pass womtool validation

• Update wdl/tasks/QC/Fingerprinting.wdl

• Update wdl/tasks/Utility/ONTUtils.wdl

Co-authored-by: Steve Huang [email protected]

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Co-authored-by: bshifaw [email protected]
Co-authored-by: Steve Huang [email protected]

lrp_3.0.73

development docs draft (#396)

• development docs draft

• added intro for docker_style_guide.md

• add to docker_style_guide.md

• add to wdl_style_guide.md

• renamed dev_guide to development_guide

• rewrote overview, added visuals for directory structure

• Minor fixes, Added Workflow Deployment in README.md

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Co-authored-by: bshifaw [email protected]

lrp_3.0.72

Fix for Repo Git Page action yml (#398)

• added make docs dir if not exist

• add graphviz as an installation requirement

• switching to mac environment

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Co-authored-by: bshifaw [email protected]

lrp_3.0.71

Automatically Generate Repository Git Page (#391)

• add git page action

• Add scripts to create dot and png files for workflows

• Add scripts to add png link to md

• Add mkdocs.yml file

• changed png link to be relative path instead of absolute.

• Added script to add header to wdl markdown, and remove task info from wdl workflow markdown

• edited wdlviz.py to add the option to name the output file by a specified name, edited create_wdl_visual.py to use wdl basename for dot file

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Co-authored-by: bshifaw [email protected]

lrp_3.0.70

New workflows to deal with ONT flowcells that have multiple basecall directories (#325)

• one workflow that essentially copies the current ONTFlowcell, but aims at a basecall directory
• one workflow that plays the role of ONTFlowcell, but actually aggregates results from the WF above

lrp_3.0.69

add miniwdl and shellcheck installation to cd.yml (#397)

Co-authored-by: bshifaw [email protected]

lrp_3.0.68

reheader FP vcfs from full hg38 to no_alt (#344)

lrp_3.0.67

Move wdl files to central directory called wdl (#393)

• moved wdls to wdl folder, updated testing location for wdl validation

• updated wdl paths in dockstore.yml

• renamed 'deprecated_wdl' to 'deprecated', updated docstore.yml accordingly

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Co-authored-by: bshifaw [email protected]

lrp_3.0.66

Standardize wdl description (#392)

• standardized pipeline/ONT workflow meta and parameter_meta bocks

• standardized pipeline/pacbio workflow meta and parameter_meta bocks

• standardized pipeline/techAgnostic workflow meta and parameter_meta bocks

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Co-authored-by: bshifaw [email protected]