From: Sarah Wait Zaranek <swz@curii.com>
Date: Thu, 25 Jun 2020 13:03:51 +0000 (+0000)
Subject: Updataing readme and yml files
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/974a6542eec937b12f7c78c308cd5dd4deee521f

Updataing readme and yml files
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

diff --git a/WGS-processing/README.md b/WGS-processing/README.md
index aa2d8e6..71ec46a 100644
--- a/WGS-processing/README.md
+++ b/WGS-processing/README.md
@@ -5,7 +5,7 @@ This directory contains an Arvados demo showing processing of whole genome seque
 * Variant calling in parallel using GATK Haplotype Caller (https://gatk.broadinstitute.org/hc/en-us)
 * Generation of an HTML report comparing variants against ClinVar archive (https://www.ncbi.nlm.nih.gov/clinvar/)
 
-Workflows are written in CWL v1.1. 
+Workflows are written in CWL v1.1. (https://www.commonwl.org/)
 
 Subdirectories are:
 * cwl - contains CWL code for the demo
@@ -15,9 +15,8 @@ Subdirectories are:
 
 To run the workflow:
 
-* cd into cwl directory
 * run the following:
-  arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml
+  arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID ./cwl/wgs-processing-wf.cwl ./yml/YOURINPUTS.yml
 
 About the Demo Data:
 WGS Data used in this demo is public data made available by the Personal Genome Project.  
diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index 58e38cb..9c1e78a 100644
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -53,7 +53,6 @@ outputs:
     outputSource: bwamem-gatk-report/gvcf
     format: edam:format_3016 # GVCF
     label: GVCFs generated from GATK 
-    
   report:
     type: File[]  
     outputSource: bwamem-gatk-report/report
diff --git a/WGS-processing/yml/bwa-gatk-report-wf-UK.yml b/WGS-processing/yml/bwamem-gatk-report-wf.yml
similarity index 100%
rename from WGS-processing/yml/bwa-gatk-report-wf-UK.yml
rename to WGS-processing/yml/bwamem-gatk-report-wf.yml
diff --git a/WGS-processing/yml/fastqc.yml b/WGS-processing/yml/fastqc.yml
new file mode 100644
index 0000000..53f4d7e
--- /dev/null
+++ b/WGS-processing/yml/fastqc.yml
@@ -0,0 +1,7 @@
+fastq1:
+  class: File
+  location: keep:c96565a96cd428fe92bf70e97488bd80+21857/ERR1726424_1.fastq/ERR1726424_1.fastq.gz
+
+fastq2:
+  class: File
+  location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
diff --git a/WGS-processing/yml/bwa-gatk-wf-WGC071838D.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC071838D.yml
similarity index 100%
rename from WGS-processing/yml/bwa-gatk-wf-WGC071838D.yml
rename to WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC071838D.yml
diff --git a/WGS-processing/yml/bwa-gatk-wf-WGC074701D.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC074701D.yml
similarity index 100%
rename from WGS-processing/yml/bwa-gatk-wf-WGC074701D.yml
rename to WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC074701D.yml
diff --git a/WGS-processing/yml/bwa-gatk-wf-chr19.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-chr19.yml
similarity index 100%
rename from WGS-processing/yml/bwa-gatk-wf-chr19.yml
rename to WGS-processing/yml/not-in-use/bwa-gatk-wf-chr19.yml
diff --git a/WGS-processing/yml/bwa-gatk-wf-report.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-report.yml
similarity index 100%
rename from WGS-processing/yml/bwa-gatk-wf-report.yml
rename to WGS-processing/yml/not-in-use/bwa-gatk-wf-report.yml
diff --git a/WGS-processing/yml/bwa-gatk-wf.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf.yml
similarity index 100%
rename from WGS-processing/yml/bwa-gatk-wf.yml
rename to WGS-processing/yml/not-in-use/bwa-gatk-wf.yml
diff --git a/WGS-processing/yml/samtools-sort-WGC069888D.yml b/WGS-processing/yml/samtools-sort.yml
similarity index 98%
rename from WGS-processing/yml/samtools-sort-WGC069888D.yml
rename to WGS-processing/yml/samtools-sort.yml
index c1904f5..7c27a9c 100644
--- a/WGS-processing/yml/samtools-sort-WGC069888D.yml
+++ b/WGS-processing/yml/samtools-sort.yml
@@ -1,4 +1,5 @@
 bam:
   class: File
   location: keep:su92l-4zz18-v4m3dx8agdp1y9r/WGC069888D.bam
+
 sample: WGC069888D
diff --git a/WGS-processing/yml/wgs-processing-wf.yml b/WGS-processing/yml/wgs-processing-wf.yml
index 8853a80..85b2ffd 100644
--- a/WGS-processing/yml/wgs-processing-wf.yml
+++ b/WGS-processing/yml/wgs-processing-wf.yml
@@ -1,5 +1,3 @@
-sample: ERR1726424
-
 reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa