arvados-tutorial.git
11 months agoBugfix .bai secondary file for ApplyBSQR behavior
Peter Amstutz [Mon, 25 Oct 2021 20:02:45 +0000 (20:02 +0000)]
Bugfix .bai secondary file for ApplyBSQR behavior

no issue #

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoMerge branch '17049-make-singlechrom'
Jiayong Li [Thu, 14 Jan 2021 22:48:51 +0000 (22:48 +0000)]
Merge branch '17049-make-singlechrom'
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
closes #17049

20 months agoAdd comments on the chr19 only yml 17049-make-singlechrom
Jiayong Li [Thu, 14 Jan 2021 22:43:03 +0000 (22:43 +0000)]
Add comments on the chr19 only yml
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
refs #17049

21 months agoAdd chr19 yml by changing fullintervallist
Jiayong Li [Mon, 28 Dec 2020 22:07:21 +0000 (22:07 +0000)]
Add chr19 yml by changing fullintervallist
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
refs #17049

21 months agoAdd workflow to generate single chromosome fastqs
Jiayong Li [Tue, 15 Dec 2020 22:33:51 +0000 (22:33 +0000)]
Add workflow to generate single chromosome fastqs
Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
refs #17049

2 years agoupdating yml
Sarah Wait Zaranek [Thu, 13 Aug 2020 12:30:13 +0000 (12:30 +0000)]
updating yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating yml for 2 vcfs of known sites
Sarah Wait Zaranek [Mon, 27 Jul 2020 20:08:24 +0000 (20:08 +0000)]
Updating yml for 2 vcfs of known sites
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoFixing labels for knownsites
Sarah Wait Zaranek [Mon, 27 Jul 2020 20:05:28 +0000 (20:05 +0000)]
Fixing labels for knownsites
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating to allow for two vcfs of known sites
Sarah Wait Zaranek [Mon, 27 Jul 2020 19:56:49 +0000 (19:56 +0000)]
Updating to allow for two vcfs of known sites
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating cwl and yml for intervals and other changes
Sarah Wait Zaranek [Thu, 23 Jul 2020 13:09:38 +0000 (13:09 +0000)]
Updating cwl and yml for intervals and other changes
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating HTML edam comments
Sarah Wait Zaranek [Tue, 14 Jul 2020 17:43:25 +0000 (17:43 +0000)]
Updating HTML edam comments
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating comments
Sarah Wait Zaranek [Sun, 12 Jul 2020 19:17:03 +0000 (19:17 +0000)]
Updating comments
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoFixing edam reference
Sarah Wait Zaranek [Sun, 12 Jul 2020 19:12:27 +0000 (19:12 +0000)]
Fixing edam reference
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoMoving #
Sarah Wait Zaranek [Fri, 10 Jul 2020 16:10:32 +0000 (16:10 +0000)]
Moving #
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating docker reference
Sarah Wait Zaranek [Tue, 7 Jul 2020 15:48:30 +0000 (15:48 +0000)]
Updating docker reference
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating bwa-samtools dockerfile
Sarah Wait Zaranek [Tue, 7 Jul 2020 15:46:14 +0000 (15:46 +0000)]
Updating bwa-samtools dockerfile
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding more formats to yml
Sarah Wait Zaranek [Tue, 7 Jul 2020 00:41:03 +0000 (00:41 +0000)]
Adding more formats to yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating yml for formats
Sarah Wait Zaranek [Tue, 7 Jul 2020 00:36:13 +0000 (00:36 +0000)]
Updating yml for formats
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoRemoving initial work dir requirement when not needed
Sarah Wait Zaranek [Fri, 3 Jul 2020 13:31:35 +0000 (13:31 +0000)]
Removing initial work dir requirement when not needed
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating yml files
Sarah Wait Zaranek [Fri, 3 Jul 2020 13:14:45 +0000 (13:14 +0000)]
Updating yml files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating yml files
Sarah Wait Zaranek [Fri, 3 Jul 2020 13:10:27 +0000 (13:10 +0000)]
Updating yml files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoRemoving white spaces and commenting out schemas
Sarah Wait Zaranek [Thu, 2 Jul 2020 17:04:01 +0000 (17:04 +0000)]
Removing white spaces and commenting out schemas
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoRemoving white space and commenting out schemas
Sarah Wait Zaranek [Thu, 2 Jul 2020 16:28:54 +0000 (16:28 +0000)]
Removing white space and commenting out schemas
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoMoving fastqc into not in use for docker containers
Sarah Wait Zaranek [Thu, 2 Jul 2020 16:19:49 +0000 (16:19 +0000)]
Moving fastqc into not in use for docker containers
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoRemoving white spaces and commenting schemas
Sarah Wait Zaranek [Thu, 2 Jul 2020 16:19:04 +0000 (16:19 +0000)]
Removing white spaces and commenting schemas
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating for new Docker containter
Sarah Wait Zaranek [Thu, 2 Jul 2020 14:50:54 +0000 (14:50 +0000)]
Updating for new Docker containter
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding links about CWL to the readme
Sarah Wait Zaranek [Wed, 1 Jul 2020 19:04:34 +0000 (19:04 +0000)]
Adding links about CWL to the readme
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoSwitching variable knownsites1 to knownsites in yml files
Sarah Wait Zaranek [Wed, 1 Jul 2020 18:59:02 +0000 (18:59 +0000)]
Switching variable knownsites1 to knownsites in yml files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoSwitching variable knownsites1 to knownsites
Sarah Wait Zaranek [Wed, 1 Jul 2020 18:56:55 +0000 (18:56 +0000)]
Switching variable knownsites1 to knownsites
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating report generation code
Sarah Wait Zaranek [Wed, 1 Jul 2020 18:51:42 +0000 (18:51 +0000)]
Updating report generation code
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating yml to include intervals
Sarah Wait Zaranek [Wed, 1 Jul 2020 18:42:43 +0000 (18:42 +0000)]
Updating yml to include intervals
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding metatdata and labels
Sarah Wait Zaranek [Wed, 1 Jul 2020 18:42:15 +0000 (18:42 +0000)]
Adding metatdata and labels
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding metadata, updating variables
Sarah Wait Zaranek [Wed, 1 Jul 2020 17:47:34 +0000 (17:47 +0000)]
Adding metadata, updating variables
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding metadata
Sarah Wait Zaranek [Wed, 1 Jul 2020 16:46:08 +0000 (16:46 +0000)]
Adding metadata
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding metadata and step renaming
Sarah Wait Zaranek [Wed, 1 Jul 2020 16:00:28 +0000 (16:00 +0000)]
Adding metadata and step renaming
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating metadata
Sarah Wait Zaranek [Wed, 1 Jul 2020 14:35:47 +0000 (14:35 +0000)]
updating metadata
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating for metadata and yml to check command line cwl
Sarah Wait Zaranek [Mon, 29 Jun 2020 21:42:02 +0000 (21:42 +0000)]
updating for metadata and yml to check command line cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding labels and metadata
Sarah Wait Zaranek [Fri, 26 Jun 2020 02:20:46 +0000 (02:20 +0000)]
Adding labels and metadata
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding arv to namespace
Sarah Wait Zaranek [Fri, 26 Jun 2020 02:00:15 +0000 (02:00 +0000)]
Adding arv to namespace
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding labels and other metadata
Sarah Wait Zaranek [Fri, 26 Jun 2020 01:52:47 +0000 (01:52 +0000)]
Adding labels and other metadata
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoremoving swp file
Sarah Wait Zaranek [Thu, 25 Jun 2020 14:43:29 +0000 (14:43 +0000)]
removing swp file
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding labels and metadata
Sarah Wait Zaranek [Thu, 25 Jun 2020 14:42:13 +0000 (14:42 +0000)]
Adding labels and metadata
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating labels and metadata
Sarah Wait Zaranek [Thu, 25 Jun 2020 13:49:58 +0000 (13:49 +0000)]
Updating labels and metadata
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoEven more formatting
Sarah Wait Zaranek [Thu, 25 Jun 2020 13:13:01 +0000 (13:13 +0000)]
Even more formatting
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoFixing formating issue
Sarah Wait Zaranek [Thu, 25 Jun 2020 13:11:14 +0000 (13:11 +0000)]
Fixing formating issue
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding Arvados info to readme
Sarah Wait Zaranek [Thu, 25 Jun 2020 13:10:08 +0000 (13:10 +0000)]
Adding Arvados info to readme
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoreorg of yml files
Sarah Wait Zaranek [Thu, 25 Jun 2020 13:06:46 +0000 (13:06 +0000)]
reorg of yml files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdataing readme and yml files
Sarah Wait Zaranek [Thu, 25 Jun 2020 13:03:51 +0000 (13:03 +0000)]
Updataing readme and yml files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating labels
Sarah Wait Zaranek [Thu, 25 Jun 2020 01:48:05 +0000 (01:48 +0000)]
Updating labels
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding more labels
Sarah Wait Zaranek [Thu, 25 Jun 2020 01:26:02 +0000 (01:26 +0000)]
Adding more labels
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding more labels/metadata
Sarah Wait Zaranek [Wed, 24 Jun 2020 23:36:02 +0000 (23:36 +0000)]
Adding more labels/metadata
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding labels and other annotations
Sarah Wait Zaranek [Wed, 24 Jun 2020 23:08:50 +0000 (23:08 +0000)]
Adding labels and other annotations
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating labels and hints on cwl
Sarah Wait Zaranek [Wed, 24 Jun 2020 19:46:10 +0000 (19:46 +0000)]
Updating labels and hints on cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding labels
Sarah Wait Zaranek [Wed, 24 Jun 2020 17:10:55 +0000 (17:10 +0000)]
Adding labels
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding labels and formats to cwl
Sarah Wait Zaranek [Wed, 24 Jun 2020 15:25:10 +0000 (15:25 +0000)]
Adding labels and formats to cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating main cwl workflow
Sarah Wait Zaranek [Tue, 23 Jun 2020 19:42:58 +0000 (19:42 +0000)]
Updating main cwl workflow
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding license info to cwl
Sarah Wait Zaranek [Tue, 23 Jun 2020 19:35:45 +0000 (19:35 +0000)]
Adding license info to cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding changes to Dockerfiles
Sarah Wait Zaranek [Tue, 23 Jun 2020 17:15:13 +0000 (17:15 +0000)]
Adding changes to Dockerfiles
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating docker file for fastqc
Sarah Wait Zaranek [Tue, 23 Jun 2020 04:40:42 +0000 (04:40 +0000)]
Updating docker file for fastqc
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating clinvar report docker file and reorganizing yml files
Sarah Wait Zaranek [Tue, 23 Jun 2020 01:41:13 +0000 (01:41 +0000)]
Updating clinvar report docker file and reorganizing yml files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating readme
Sarah Wait Zaranek [Fri, 19 Jun 2020 21:07:50 +0000 (21:07 +0000)]
Updating readme
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating licenseignore
Sarah Wait Zaranek [Fri, 19 Jun 2020 21:02:48 +0000 (21:02 +0000)]
Updating licenseignore
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoMoving license location
Sarah Wait Zaranek [Fri, 19 Jun 2020 21:01:38 +0000 (21:01 +0000)]
Moving license location
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding license and licenseignore
Sarah Wait Zaranek [Fri, 19 Jun 2020 21:00:09 +0000 (21:00 +0000)]
Adding license and licenseignore
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating readme
Sarah Wait Zaranek [Fri, 19 Jun 2020 20:54:20 +0000 (20:54 +0000)]
Updating readme
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoMoving readme to markdown
Sarah Wait Zaranek [Fri, 19 Jun 2020 20:49:38 +0000 (20:49 +0000)]
Moving readme to markdown
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating not-in-use directory
Sarah Wait Zaranek [Thu, 18 Jun 2020 14:17:21 +0000 (14:17 +0000)]
Updating not-in-use directory
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating dockerfiles
Sarah Wait Zaranek [Thu, 18 Jun 2020 01:04:03 +0000 (01:04 +0000)]
Updating dockerfiles
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoremoving un-needed yml
Sarah Wait Zaranek [Thu, 18 Jun 2020 00:59:37 +0000 (00:59 +0000)]
removing un-needed yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agocleaning up src files
Sarah Wait Zaranek [Thu, 18 Jun 2020 00:56:12 +0000 (00:56 +0000)]
cleaning up src files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating readme and reorganization
Sarah Wait Zaranek [Thu, 18 Jun 2020 00:52:51 +0000 (00:52 +0000)]
Updating readme and reorganization
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating links to "helper" cwl
Sarah Wait Zaranek [Wed, 17 Jun 2020 18:17:25 +0000 (18:17 +0000)]
Updating links to "helper" cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdd scatter wf for overall scatter
Sarah Wait Zaranek [Wed, 17 Jun 2020 17:13:54 +0000 (17:13 +0000)]
Add scatter wf for overall scatter
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding readme and clean up
Sarah Wait Zaranek [Wed, 17 Jun 2020 16:47:27 +0000 (16:47 +0000)]
Adding readme and clean up
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoRearranging for clarity
Sarah Wait Zaranek [Wed, 17 Jun 2020 16:20:39 +0000 (16:20 +0000)]
Rearranging for clarity
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoremoving src code not in use
Sarah Wait Zaranek [Tue, 16 Jun 2020 01:42:38 +0000 (01:42 +0000)]
removing src code not in use
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoyml to get fastq from directory
Sarah Wait Zaranek [Tue, 16 Jun 2020 01:41:05 +0000 (01:41 +0000)]
yml to get fastq from directory
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding code to get fastqs from directory
Sarah Wait Zaranek [Tue, 16 Jun 2020 01:40:20 +0000 (01:40 +0000)]
Adding code to get fastqs from directory
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating yml
Sarah Wait Zaranek [Mon, 15 Jun 2020 21:54:19 +0000 (21:54 +0000)]
updating yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding modified code to select variants and gather arrays
Sarah Wait Zaranek [Thu, 11 Jun 2020 19:58:06 +0000 (19:58 +0000)]
Adding modified code to select variants and gather arrays
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding files for gathering gvcfs and cleaning gvcfs
Sarah Wait Zaranek [Thu, 28 May 2020 01:39:28 +0000 (01:39 +0000)]
Adding files for gathering gvcfs and cleaning gvcfs
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding yml files for gathering and intervals
Sarah Wait Zaranek [Fri, 22 May 2020 13:11:22 +0000 (13:11 +0000)]
Adding yml files for gathering and intervals
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding gather cwls
Sarah Wait Zaranek [Fri, 22 May 2020 13:06:10 +0000 (13:06 +0000)]
Adding gather cwls
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoadding helper directory for structure, may reorg later
Sarah Wait Zaranek [Fri, 8 May 2020 07:42:30 +0000 (07:42 +0000)]
adding helper directory for structure, may reorg later
adding cwl to do intervals and scattering
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoadding base recalibrator yml and updating bwamem yml
Sarah Wait Zaranek [Thu, 30 Apr 2020 00:41:03 +0000 (00:41 +0000)]
adding base recalibrator yml and updating bwamem yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating bwamem CWL and adding base recalibrator cwl
Sarah Wait Zaranek [Thu, 30 Apr 2020 00:40:18 +0000 (00:40 +0000)]
Updating bwamem CWL and adding base recalibrator cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoremoving unnecessary step, renaming cwl file
Sarah Wait Zaranek [Wed, 29 Apr 2020 01:26:10 +0000 (01:26 +0000)]
removing unnecessary step, renaming cwl file
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating yml to include UK pgp example
Sarah Wait Zaranek [Tue, 21 Apr 2020 01:32:04 +0000 (01:32 +0000)]
updating yml to include UK pgp example
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating cwl
Sarah Wait Zaranek [Tue, 21 Apr 2020 01:31:20 +0000 (01:31 +0000)]
updating cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating dockerfiles
Sarah Wait Zaranek [Wed, 1 Apr 2020 03:40:07 +0000 (03:40 +0000)]
updating dockerfiles
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating yml
Sarah Wait Zaranek [Wed, 1 Apr 2020 03:39:45 +0000 (03:39 +0000)]
updating yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating annotation and gatk code
Sarah Wait Zaranek [Wed, 1 Apr 2020 03:39:07 +0000 (03:39 +0000)]
Updating annotation and gatk code
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoupdating preprocessing code
Sarah Wait Zaranek [Wed, 1 Apr 2020 03:38:30 +0000 (03:38 +0000)]
updating preprocessing code
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding ploidy code
Sarah Wait Zaranek [Wed, 1 Apr 2020 03:37:36 +0000 (03:37 +0000)]
Adding ploidy code
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating yml
Sarah Wait Zaranek [Wed, 11 Mar 2020 15:04:35 +0000 (15:04 +0000)]
Updating yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating CWL for overarching workflow
Sarah Wait Zaranek [Wed, 11 Mar 2020 15:04:04 +0000 (15:04 +0000)]
Updating CWL for overarching workflow
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agocleaning up src directory and updating head.html
Sarah Wait Zaranek [Fri, 6 Mar 2020 08:43:54 +0000 (08:43 +0000)]
cleaning up src directory and updating head.html
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding cwl to convert gvcf to vcf
Sarah Wait Zaranek [Fri, 6 Mar 2020 08:42:59 +0000 (08:42 +0000)]
Adding cwl to convert gvcf to vcf
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating cwl
Sarah Wait Zaranek [Thu, 5 Mar 2020 18:13:22 +0000 (18:13 +0000)]
Updating cwl
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding cwl to annotate and generate report
Sarah Wait Zaranek [Thu, 5 Mar 2020 13:44:51 +0000 (13:44 +0000)]
Adding cwl to annotate and generate report
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #