Multiqc

[robinandeer]

Add support for MultiQC
It's very basic to begin with

This will go together with a more dedicated plugin which will format the report to work well with Scout and the data it usually imports.

This is my BOSC 2017 code project 👾

[vwirta]

Wow!

…

Sent from my iPhone

On 20 Jul 2017, at 17:49, Robin Andeer ***@***.***> wrote: Add support for MultiQC It's very basic to begin with This will go together with a more dedicated plugin which will format the report to work well with Scout and the data it usually imports. This is my BOSC 2017 code project 👾 You can view, comment on, or merge this pull request online at: #564 Commit Summary list cases within each group in separate table 👨‍👩‍👧‍👦 show link to cancer variants if relevant on cases list display number of individuals on case overview if more than 1 show warning if HGNC symbol doesn't exist, see #528 handle decimals written using "," or "." the same in filter forms, #fix 519 update exac override option to default=False open link as external, fix #511 show display name of institute when sharing and revoking a shared case, fix #504 add default number of total archived cases add proxy fix to auto start module update parsing of custom panel Get overlapping variants with coordinates instead of hgnc symbols Check if gene object exists Updates tests for get overlapping Fix #520 display notice on variants view if variant has been commented on, fix #535 fix calls to updated parse variant fix display of clinsig annotations, fix #483 display exon/intron count dynamically in sanger email add users view, fix #543 add filter option "local obs" to the SNV filter UI hide case groups without cases Adds acmg algorithm add acmg selection from variant develop acmg critera selection view prepare event function call to submit classification Adds acmg criterias do docs rename US to VUS Adds API to store and retreive evaluations Adds tests for pathogenic evaluation Adds tests for Likely pathogenic, benign and likely benign Adds tests for get_acmg update determination of acmg classification in UI Add the ACMG classification to variant when submitting classification Adds get_evaluation and delete_evaluation add views to view and delete evaluation finish ACMG editor Merge pull request #538 from Clinical-Genomics/acmg-ui add upload gene panel, fix #465 Merge pull request #544 from Clinical-Genomics/upload-panel Adds functionality to check if a variant is in the PAR regions Adds is_par to adapter.variant(). Fix #541 fix issue on variant page when acmg classification is missing display PAR label for certain variants, fix #545 display genes and functional annotations as a list in overview Merge pull request #545 from Clinical-Genomics/display-par fix filling in expected inheritance models on variant page, fix #539 add form to update default gene panels on a case Completes function `adapter.update_default_panels` Merge pull request #546 from Clinical-Genomics/switch-default-panel udpate display of inheritance and penetrance annotations add deploy script add local obs to variants view popup (archive), fix #292 add example variant tags fix issue when no phenotype terms exist Adds indexes in scout setup update docs with info on gene panel upload Updates tests to new disease interface add link to docs from panel upload form, fix #526 Updates tests Merge pull request #551 from Clinical-Genomics/rank-variants-when-loading starts parsing of peddy output Updates individual model Display variant autozygosity calls from rhocall. Qual is float. Fold away from view if not present. Faked an autozygous region call in demo case. Updated variant INFO interface for autozygosity. Nailed var INFO interface for autozygosity. Updates how cases are loaded into scout Adds command to upload variants from different resources from command line Adds peddy data to demo files Adds peddy to parsing of case Adds peddy information to buildt individuals. Fix #508 Updates test_case_handling Updates event tests Updates build tests Adds peddy files to demo data add icons and stuff to ind table Merge pull request #554 from Clinical-Genomics/add-peddy-support Adds padding of 5000 bases when loading all variants from a gene Merge pull request #555 from Clinical-Genomics/load-larger-region Merge pull request #536 from Clinical-Genomics/get_ovelapping update manual rank options, fix #512 fix smaller bugs on handling exceptions move delete button so it's not called on "enter" add endpoint for displaying multiqc report for a case add support in config for adding multiqc when loading/updating a case File Changes M docs/SUMMARY.md (1) A docs/static/scout-3-panel-file-example.csv (1) A docs/static/scout-3-panel-file-example.xlsx (0) A docs/user-guide/acmg-criterias.md (175) M docs/user-guide/panels.md (11) A scout/adapter/mongo/acmg.py (100) M scout/adapter/mongo/base.py (8) M scout/adapter/mongo/case.py (66) M scout/adapter/mongo/event.py (87) M scout/adapter/mongo/hpo.py (8) M scout/adapter/mongo/query.py (27) M scout/adapter/mongo/variant.py (90) A scout/build/acmg.py (48) M scout/build/individual.py (3) M scout/build/variant.py (7) M scout/commands/load/case.py (124) M scout/commands/load/load_database.py (2) M scout/commands/load/research.py (62) A scout/commands/load/variants.py (102) M scout/commands/setup/setup_scout.py (161) M scout/commands/update/case.py (10) M scout/commands/view/view_command.py (60) M scout/constants/__init__.py (89) A scout/constants/acmg.py (134) M scout/demo/643594.clinical.vcf.gz (0) M scout/demo/643594.clinical.vcf.gz.tbi (0) M scout/demo/643594.config.yaml (5) A scout/demo/643594.ped_check.csv (4) A scout/demo/643594.peddy.ped (4) A scout/demo/643594.sex_check.csv (4) M scout/demo/resources/ensembl_transcripts_reduced.txt.gz (0) M scout/demo/resources/hgnc_reduced_set.txt.gz (0) A scout/models/acmg_evaluation.py (28) M scout/models/case/case.py (6) M scout/models/event.py (2) M scout/models/variant/variant.py (3) M scout/parse/case.py (153) A scout/parse/peddy.py (146) M scout/parse/variant/variant.py (10) M scout/server/auto.py (4) M scout/server/blueprints/cases/controllers.py (30) M scout/server/blueprints/cases/templates/cases/actionbar.html (23) M scout/server/blueprints/cases/templates/cases/case.html (85) M scout/server/blueprints/cases/templates/cases/cases.html (59) M scout/server/blueprints/cases/views.py (24) A scout/server/blueprints/login/controllers.py (31) A scout/server/blueprints/login/static/commander.svg (1103) A scout/server/blueprints/login/static/commissioner.svg (1705) A scout/server/blueprints/login/static/constable.svg (20) A scout/server/blueprints/login/static/inspector.svg (166) A scout/server/blueprints/login/static/sergeant.svg (26) A scout/server/blueprints/login/static/superintendent.svg (450) A scout/server/blueprints/login/templates/login/users.html (52) M scout/server/blueprints/login/views.py (26) M scout/server/blueprints/panels/templates/panels/panels.html (1) M scout/server/blueprints/variants/controllers.py (152) M scout/server/blueprints/variants/forms.py (32) A scout/server/blueprints/variants/templates/variants/acmg.html (112) M scout/server/blueprints/variants/templates/variants/cancer-variants.html (9) M scout/server/blueprints/variants/templates/variants/components.html (33) M scout/server/blueprints/variants/templates/variants/sv-variant.html (2) M scout/server/blueprints/variants/templates/variants/variant.html (204) M scout/server/blueprints/variants/templates/variants/variants.html (53) M scout/server/blueprints/variants/views.py (109) M scout/server/static/styles.css (96) M scout/server/templates/layout.html (3) M scout/server/userpanel.py (4) A scout/utils/acmg.py (219) A scout/utils/convert.py (35) A scout/utils/par.py (20) A scripts/deploy (1) M tasks.py (6) M tests/adapter/test_case_handling.py (8) M tests/adapter/test_event_handling.py (64) M tests/adapter/test_hpo_handler.py (53) M tests/adapter/test_query.py (37) M tests/adapter/test_variant_handling.py (21) M tests/build/test_build_individual.py (3) M tests/conftest.py (6) M tests/load/test_load_case.py (6) M tests/load/test_load_hpo.py (22) D tests/load/test_load_scout.py (13) A tests/utils/test_acmg.py (385) A tests/utils/test_par.py (47) Patch Links: https://github.com/Clinical-Genomics/scout/pull/564.patch https://github.com/Clinical-Genomics/scout/pull/564.diff — You are receiving this because you are subscribed to this thread. 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[henrikstranneheim]

Nice! /H