diff --git a/docs/reference/fileformats/assay.md b/docs/reference/fileformats/assay.md new file mode 100644 index 00000000..a506e066 --- /dev/null +++ b/docs/reference/fileformats/assay.md @@ -0,0 +1 @@ +::: genie_registry.assay \ No newline at end of file diff --git a/docs/reference/fileformats/bed.md b/docs/reference/fileformats/bed.md new file mode 100644 index 00000000..4873808a --- /dev/null +++ b/docs/reference/fileformats/bed.md @@ -0,0 +1 @@ +::: genie_registry.bed \ No newline at end of file diff --git a/docs/reference/fileformats/clinical.md b/docs/reference/fileformats/clinical.md new file mode 100644 index 00000000..fc132126 --- /dev/null +++ b/docs/reference/fileformats/clinical.md @@ -0,0 +1 @@ +::: genie_registry.clinical \ No newline at end of file diff --git a/docs/reference/fileformats/cna.md b/docs/reference/fileformats/cna.md new file mode 100644 index 00000000..a17d36fa --- /dev/null +++ b/docs/reference/fileformats/cna.md @@ -0,0 +1 @@ +::: genie_registry.cna \ No newline at end of file diff --git a/docs/reference/fileformats/mutations_in_cis.md b/docs/reference/fileformats/mutations_in_cis.md new file mode 100644 index 00000000..9fd6e694 --- /dev/null +++ b/docs/reference/fileformats/mutations_in_cis.md @@ -0,0 +1 @@ +::: genie_registry.mutationsInCis \ No newline at end of file diff --git a/docs/reference/fileformats/patient_retraction.md b/docs/reference/fileformats/patient_retraction.md new file mode 100644 index 00000000..87ddab89 --- /dev/null +++ b/docs/reference/fileformats/patient_retraction.md @@ -0,0 +1 @@ +::: genie_registry.patientRetraction \ No newline at end of file diff --git a/docs/reference/fileformats/sample_retraction.md b/docs/reference/fileformats/sample_retraction.md new file mode 100644 index 00000000..75d55d07 --- /dev/null +++ b/docs/reference/fileformats/sample_retraction.md @@ -0,0 +1 @@ +::: genie_registry.sampleRetraction \ No newline at end of file diff --git a/docs/reference/fileformats/seg.md b/docs/reference/fileformats/seg.md new file mode 100644 index 00000000..1fcadbda --- /dev/null +++ b/docs/reference/fileformats/seg.md @@ -0,0 +1 @@ +::: genie_registry.seg \ No newline at end of file diff --git a/docs/reference/fileformats/structural_variant.md b/docs/reference/fileformats/structural_variant.md new file mode 100644 index 00000000..4f834231 --- /dev/null +++ b/docs/reference/fileformats/structural_variant.md @@ -0,0 +1 @@ +::: genie_registry.structural_variant \ No newline at end of file diff --git a/docs/reference/fileformats/vcf.md b/docs/reference/fileformats/vcf.md new file mode 100644 index 00000000..ecee8a99 --- /dev/null +++ b/docs/reference/fileformats/vcf.md @@ -0,0 +1 @@ +::: genie_registry.vcf \ No newline at end of file diff --git a/docs/reference/fileformats/workflow.md b/docs/reference/fileformats/workflow.md new file mode 100644 index 00000000..ccdaa040 --- /dev/null +++ b/docs/reference/fileformats/workflow.md @@ -0,0 +1 @@ +::: genie_registry.workflow \ No newline at end of file diff --git a/docs/reference/helper_modules/create_case_lists.md b/docs/reference/helper_modules/create_case_lists.md new file mode 100644 index 00000000..eb26f186 --- /dev/null +++ b/docs/reference/helper_modules/create_case_lists.md @@ -0,0 +1 @@ +::: genie.create_case_lists \ No newline at end of file diff --git a/docs/reference/helper_modules/dashboard_table_updater.md b/docs/reference/helper_modules/dashboard_table_updater.md new file mode 100644 index 00000000..542f8d6d --- /dev/null +++ b/docs/reference/helper_modules/dashboard_table_updater.md @@ -0,0 +1 @@ +::: genie.dashboard_table_updater \ No newline at end of file diff --git a/docs/reference/main_pipeline_commands/consortium_to_public.md b/docs/reference/main_pipeline_commands/consortium_to_public.md new file mode 100644 index 00000000..41adf69b --- /dev/null +++ b/docs/reference/main_pipeline_commands/consortium_to_public.md @@ -0,0 +1 @@ +::: bin.consortium_to_public \ No newline at end of file diff --git a/docs/reference/main_pipeline_commands/database_to_staging.md b/docs/reference/main_pipeline_commands/database_to_staging.md new file mode 100644 index 00000000..fcece6de --- /dev/null +++ b/docs/reference/main_pipeline_commands/database_to_staging.md @@ -0,0 +1 @@ +::: bin.database_to_staging \ No newline at end of file diff --git a/docs/reference/main_pipeline_commands/input_to_database.md b/docs/reference/main_pipeline_commands/input_to_database.md new file mode 100644 index 00000000..4933515b --- /dev/null +++ b/docs/reference/main_pipeline_commands/input_to_database.md @@ -0,0 +1 @@ +::: bin.input_to_database \ No newline at end of file diff --git a/docs/reference/main_pipeline_steps/input_to_database.md b/docs/reference/main_pipeline_steps/input_to_database/input_to_database.md similarity index 100% rename from docs/reference/main_pipeline_steps/input_to_database.md rename to docs/reference/main_pipeline_steps/input_to_database/input_to_database.md diff --git a/docs/reference/helper_modules/process_mutation.md b/docs/reference/main_pipeline_steps/input_to_database/process_mutation.md similarity index 100% rename from docs/reference/helper_modules/process_mutation.md rename to docs/reference/main_pipeline_steps/input_to_database/process_mutation.md diff --git a/docs/reference/main_pipeline_steps/input_to_database/to_retract.md b/docs/reference/main_pipeline_steps/input_to_database/to_retract.md new file mode 100644 index 00000000..aaae692e --- /dev/null +++ b/docs/reference/main_pipeline_steps/input_to_database/to_retract.md @@ -0,0 +1 @@ +::: genie.toRetract \ No newline at end of file diff --git a/docs/reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md b/docs/reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md new file mode 100644 index 00000000..f93d5106 --- /dev/null +++ b/docs/reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md @@ -0,0 +1 @@ +::: genie.write_invalid_reasons \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 257e75f0..602c2ce0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -16,21 +16,46 @@ nav: - Getting Started: getting_started.md - Tutorials: - Local File Validation: tutorials/local_file_validation.md - - Reference: + - Reference: + # contains reference to all of the technical codebase + - Main Pipeline Commands: + # contains reference to the scripts with the command line args we call to + # run the pipeline + - Input to Database: reference/main_pipeline_commands/input_to_database.md + - Database to Staging: reference/main_pipeline_commands/database_to_staging.md + - Consortium to Public: reference/main_pipeline_commands/consortium_to_public.md - Main Pipeline Steps: - - Input to Database: reference/main_pipeline_steps/input_to_database.md + # contains all code related to input to database step + - Input to Database: + - input_to_database: reference/main_pipeline_steps/input_to_database/input_to_database.md + - validate: reference/main_pipeline_steps/input_to_database/validate.md + - write_invalid_reasons: reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md + - process_mutation: reference/main_pipeline_steps/input_to_database/process_mutation.md + - to_retract: reference/main_pipeline_steps/input_to_database/toRetract.py - Database to Staging: reference/main_pipeline_steps/database_to_staging.md - Consortium to Public: reference/main_pipeline_steps/consortium_to_public.md - Fileformats: - Fileformat: reference/fileformats/fileformat.md - - maf: reference/fileformats/maf.md + - Assay Information: reference/fileformats/assay.md + - Bed: reference/fileformats/bed.md + - Clinical: reference/fileformats/clinical.md + - Cna: reference/fileformats/cna.md + - Maf: reference/fileformats/maf.md + - Mutations In Cis: reference/fileformats/mutations_in_cis.md + - Patient retraction: reference/fileformats/patient_retraction.md + - Sample retraction: reference/fileformats/sample_retraction.md + - Segmented: reference/fileformats/seg.md + - Structural variant: reference/fileformats/structural_variant.md + - Vcf: reference/fileformats/vcf.md + - Workflow: reference/fileformats/workflow.md - Helper modules: - - process_functions: reference/helper_modules/process_functions.md - - validate: reference/helper_modules/validate.md + # contains all code used in more than one step of the pipeline + - create_case_lists: reference/helper_modules/create_case_lists.md + - dashboard_table_updater: reference/helper_modules/dashboard_table_updater.md - extract: reference/helper_modules/extract.md - load: reference/helper_modules/load.md + - process_functions: reference/helper_modules/process_functions.md - transform: reference/helper_modules/transform.md - - process_mutation: reference/helper_modules/process_mutation.md # Theme configuration theme: @@ -84,6 +109,7 @@ plugins: python: options: members_order: source + # shows all functions and attributes even hidden members: yes show_if_no_docstring: False show_root_heading: True