add cram support (#1908, #1914)

CHANGELOG.rst

@@ -19,6 +19,8 @@ Added
     - UI tests for project details card (#1902)
 - **Samplesheets**
     - ``IrodsDataRequest`` timeline event extra data (#1912)
+    - CRAM file support in study apps (#1908)
+    - ``check_igv_file_suffix()`` helper in ``studyapps.utils`` (#1908)
 - **Taskflowbackend**
     - Django settings in siteinfo (#1901)
     - ``BatchSetAccessTask`` in iRODS tasks (#1905)
@@ -64,6 +66,7 @@ Fixed
     - ``IrodsDataRequest._validate_action()`` failing with ``delete`` action (#1858)
     - Protocol ref editable for new row if disabled in column config (#1875)
     - Sheet template creation failure with slash characters in title/ID fields (#1896)
+    - ``get_pedigree_file_path()`` used in cancer study app tests (#1914)
 - **Taskflowbackend**
     - Hardcoded iRODS path length in ``landing_zone_move`` (#1888)
     - Uncaught exceptions in ``SetAccessTask`` (#1906)

config/settings/base.py

@@ -807,11 +807,11 @@ def set_logging(level=None):
 # Remote sample sheet sync interval in minutes
 SHEETS_SYNC_INTERVAL = env.int('SHEETS_SYNC_INTERVAL', 5)
 
-# BAM file name suffixes to omit from study shortcuts and IGV session generation
+# BAM/CRAM file name suffixes to omit from study shortcuts and IGV sessions
 SHEETS_IGV_OMIT_BAM = env.list(
     'SHEETS_IGV_OMIT_BAM', default=['dragen_evidence.bam']
 )
-# VCF file name suffixes to omit from study shortcuts and IGV session generation
+# VCF file name suffixes to omit from study shortcuts and IGV sessions
 SHEETS_IGV_OMIT_VCF = env.list(
     'SHEETS_IGV_OMIT_VCF', default=['cnv.vcf.gz', 'ploidy.vcf.gz', 'sv.vcf.gz']
 )

docs_manual/source/admin_settings.rst

@@ -193,7 +193,7 @@ Sample Sheets Settings
 ``SHEETS_SYNC_INTERVAL``
     Interval for remote sheet synchronization in minutes (integer).
 ``SHEETS_IGV_OMIT_BAM``
-    BAM file name suffixes to omit from study shortcuts and IGV session
+    BAM and CRAM file name suffixes to omit from study shortcuts and IGV session
     generation.
 ``SHEETS_IGV_OMIT_VCF``
     VCF file name suffixes to omit from study shortcuts and IGV session

docs_manual/source/ext_tool_igv_opening.rst

@@ -35,8 +35,8 @@ The IGV session can be opened replacing the currently open session in IGV.
 Another option is to merge the session into the currently open one with the
 button displaying a plus icon.
 
-BAM and VCF files can be similarly loaded into the currently open IGV session by
-clicking the corresponding button with a plus icon.
+BAM/CRAM and VCF files can be similarly loaded into the currently open IGV
+session by clicking the corresponding button with a plus icon.
 
 .. image:: _static/ext_tool_igv/IGV_Study_Shortcuts.png
     :width: 75%
@@ -49,8 +49,8 @@ Obtaining File URLs
 You can also obtain URLs into the SODAR file serving sub system.
 
 The donor or pedigree names in the IGV links window depicted above link directly
-to the BAM and VCF files in the file serving sub system. Right-click the link
-and use the "copy link location" context menu entry to copy the File URL.
+to the BAM/CRAM and VCF files in the file serving sub system. Right-click the
+link and use the "copy link location" context menu entry to copy the File URL.
 
 You can then open this link in IGV using the "File" > "Load from URL" command.
 Paste the URL that you just copied into the "File URL" field of the window that

docs_manual/source/introduction.rst

@@ -81,7 +81,7 @@ Notable Features
     * Sample sheet generation from templates
     * Sample sheet editing and version control
     * Sample sheet export in ISA-Tab and Excel formats
-    * Automated iRODS shortcut generation for e.g. BAM/VCF files
+    * Automated iRODS shortcut generation for BAM/CRAM/VCF files
     * Automated Integrative Genomics Viewer (IGV) session file generation and
       merging
     * Track hub management for UCSC Genome Browser integration

docs_manual/source/metadata_advanced.rst

@@ -26,11 +26,13 @@ SODAR currently supports the following study configurations:
 - **Cancer**
     * Indended for: Cancer studies
     * Configuration: ``bih_cancer``
-    * Provides: **sample specific** shortcuts to the latest BAM and VCF files.
+    * Provides: **sample specific** shortcuts to the latest BAM/CRAM and VCF
+      files.
 - **Germline**
     * Indended for: Germline studies
     * Configuration: ``bih_germline``
-    * Provides: **pedigree specific** shortcuts to the latest BAM and VCF files.
+    * Provides: **pedigree specific** shortcuts to the latest BAM/CRAM and VCF
+      files.
 
 If the configuration is not specified or is not known to SODAR, the shortcut
 column will not be visible.
@@ -44,11 +46,12 @@ Placement of files in subcollections under the row-specific collection does not
 affect study shortcuts or IGV session inclusion. This also means files can be
 freely organized within desired subcollections.
 
-If there is need to omit BAM or VCF files with certain file name patterns from
-shortcuts and IGV sessions, file name suffixes can be defined in the
+If there is need to omit BAM/CRAM or VCF files with certain file name patterns
+from shortcuts and IGV sessions, file name suffixes can be defined in the
 :ref:`project update view <ui_project_update>`. Administrators can also define
 site-wide file suffixes to omit via :ref:`Django settings <admin_settings>`
-under ``SHEETS_IGV_OMIT_BAM`` and ``SHEETS_IGV_OMIT_VCF``.
+under ``SHEETS_IGV_OMIT_BAM`` (also affects CRAM files) and
+``SHEETS_IGV_OMIT_VCF``.
 
 
 Assay iRODS Data Linking

docs_manual/source/sodar_release_notes.rst

@@ -13,6 +13,7 @@ v0.14.2 (WIP)
 
 Release for minor updates, maintenance and bug fixes.
 
+- Add CRAM file support for cancer/germline study links and IGV sessions
 - Add assay plugin shortcut collection creation in landing zones
 - Add iRODS data request details in timeline events
 - Add landing zone statistics in siteinfo
@@ -25,6 +26,17 @@ Release for minor updates, maintenance and bug fixes.
 - Minor updates and bug fixes
 - Upgrade to SODAR Core v0.13.4
 
+Migration Guide
+---------------
+
+CRAM File Support
+    This release adds support for CRAM files. They are linked in studies and IGV
+    sessions similar to BAM files. If your project contains CRAM files uploaded
+    prior to this release, you will have to run :guilabel:`Update Sheet Cache`
+    in the Sample Sheets app to enable the files in study links and generated
+    IGV sessions. Alternatively, an administrator can run the ``synccache``
+    management command to update all projects or a specific project.
+
 
 v0.14.1 (2023-12-12)
 ====================

docs_manual/source/ui_project_update.rst

@@ -53,9 +53,9 @@ Token for Sheet Synchronization
 IGV session genome
     Genome used in generating IGV session files for the project. The name needs
     to be in a format accepted by IGV. Affects cancer and germline projects.
-BAM files to omit from IGV sessions
-    Comma separated list of BAM file suffixes to omit from IGV sessions.
-    Overrides site-wide setting, affects cancer and germline projects.
+BAM and CRAM files to omit from IGV sessions
+    Comma separated list of BAM and CRAM file suffixes to omit from IGV
+    sessions. Overrides site-wide setting, affects cancer and germline projects.
 VCF files to omit from IGV sessions
     Comma separated list of VCF file suffixes to omit from IGV sessions.
     Overrides site-wide setting, affects cancer and germline projects.

samplesheets/plugins.py

@@ -213,12 +213,12 @@ class ProjectAppPlugin(
         'igv_omit_bam': {
             'scope': SODAR_CONSTANTS['APP_SETTING_SCOPE_PROJECT'],
             'type': 'STRING',
-            'label': 'BAM files to omit from IGV sessions',
+            'label': 'BAM and CRAM files to omit from IGV sessions',
             'default': '',
             'placeholder': ', '.join(settings.SHEETS_IGV_OMIT_BAM),
-            'description': 'Comma separated list of BAM file suffixes to omit '
-            'from generated IGV sessions. Overrides site-wide setting, affects '
-            'cancer and germline projects.',
+            'description': 'Comma separated list of BAM and CRAM file suffixes '
+            'to omit from generated IGV sessions. Overrides site-wide setting, '
+            'affects cancer and germline projects.',
             'user_modifiable': True,
         },
         'igv_omit_vcf': {

samplesheets/studyapps/cancer/plugins.py

@@ -85,8 +85,8 @@ def get_shortcut_column(self, study, study_tables):
                 'files': {
                     'type': 'modal',
                     'icon': 'mdi:folder-open-outline',
-                    'title': 'View links to BAM, VCF and IGV session files '
-                    'for the case',
+                    'title': 'View links to BAM/CRAM, VCF and IGV session '
+                    'files for the case',
                 },
             },
             'data': [],
@@ -172,7 +172,7 @@ def get_shortcut_links(self, study, study_tables, **kwargs):
             'title': 'Case-Wise Links for {}'.format(case_id),
             'data': {
                 'session': {'title': 'IGV Session File', 'files': []},
-                'bam': {'title': 'BAM Files', 'files': []},
+                'bam': {'title': 'BAM/CRAM Files', 'files': []},
                 'vcf': {'title': 'VCF Files', 'files': []},
             },
         }
@@ -190,7 +190,7 @@ def _add_lib_path(library_name, file_type):
                         'extra_links': [
                             {
                                 'label': 'Add {} file to IGV'.format(
-                                    file_type.upper()
+                                    'BAM/CRAM' if file_type == 'bam' else 'VCF'
                                 ),
                                 'icon': 'mdi:plus-thick',
                                 'url': get_igv_irods_url(path, merge=True),