arvados-tutorial.git
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 #