arvados-tutorial.git
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 #

2 years agoUpdating files
Sarah Wait Zaranek [Thu, 27 Feb 2020 19:07:01 +0000 (19:07 +0000)]
Updating files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoMerge branch 'master' of git.arvados.org:arvados-tutorial
Sarah Wait Zaranek [Thu, 27 Feb 2020 19:04:23 +0000 (19:04 +0000)]
Merge branch 'master' of git.arvados.org:arvados-tutorial

2 years agoRearranging Folders
Sarah Wait Zaranek [Thu, 27 Feb 2020 18:56:16 +0000 (18:56 +0000)]
Rearranging Folders
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoRemoving old annotation code
Sarah Wait Zaranek [Thu, 27 Feb 2020 18:54:54 +0000 (18:54 +0000)]
Removing old annotation code
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoUpdating report python code and removing vep step from workflow
Sarah Wait Zaranek [Thu, 27 Feb 2020 18:52:56 +0000 (18:52 +0000)]
Updating report python code and removing vep step from workflow
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoArvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
Sarah Wait Zaranek [Wed, 26 Feb 2020 19:14:08 +0000 (19:14 +0000)]
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

2 years agoAdding in progress code for annotation
Sarah Wait Zaranek [Tue, 25 Feb 2020 02:00:02 +0000 (02:00 +0000)]
Adding in progress code for annotation
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <sarah@curii.com>
no issue #