From: Sarah Wait Zaranek <swz@curii.com>
Date: Thu, 18 Jun 2020 00:59:37 +0000 (+0000)
Subject: removing un-needed yml
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/86396f63fa01b893ebb174c27929f3d791846440

removing un-needed yml
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

diff --git a/WGS-processing/README b/WGS-processing/README
index 5b4b9b9..507fb3a 100644
--- a/WGS-processing/README
+++ b/WGS-processing/README
@@ -7,6 +7,12 @@ This directory contains an Arvados demo showing processing of whole genome seque
 
 Workflows are written in CWL v1.1. 
 
+Subdirectories are:
+cwl - contains CWL code for the demo
+yml - contains yml inputs for cwl demo code
+src - contains any src code for the demo
+docker - contains dockerfiles necessary to re-create any needed docker images 
+
 To run the workflow:
 
 1. cd into cwl directory
@@ -14,11 +20,5 @@ To run the workflow:
 2. run the following:
 arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml
 
-Subdirectories are:
-cwl - contains CWL code for the demo
-yml - contains yml inputs for cwl demo code
-src - contains any src code for the demo
-docker - contains dockerfiles necessary to re-create any needed docker images 
-
 About the Demo Data:
 WGS Data used in this demo is public data made available by the Personal Genome Project.  This data is from the PGP-UK (https://www.personalgenomes.org.uk/). 
diff --git a/WGS-processing/yml/check-sam.yml b/WGS-processing/yml/check-sam.yml
deleted file mode 100644
index e87a841..0000000
--- a/WGS-processing/yml/check-sam.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-sam:
-  class: File
-  location: keep:147b9da57ceb51de9d653e870d8c019a+712/hu297A5D_AE2CH6SK4DG.bam
-
-reference:
-  class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
diff --git a/WGS-processing/yml/gather-vcf2.yml b/WGS-processing/yml/gather-vcf2.yml
deleted file mode 100644
index 5f4e324..0000000
--- a/WGS-processing/yml/gather-vcf2.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-reference:
-  class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
-sample: ERR1726424
-gvcf1:
-  class: File
-  location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf.gz 
-
-gvcf2:
-  class: File
-  location: keep:054cb90cfb20dedb862af1fdd636ad3f+297/ERR1726424_10.gatk.g.vcf.gz
-
-