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 aa2d8e687cab773cca3f921d77fce9720198f6aa..71ec46a7ec776b4e16d1e186adfc447d1fbf22bc 100644 (file)
--- 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/)
 
 * 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
 
 Subdirectories are:
 * cwl - contains CWL code for the demo


@@ -15,9 +15,8 @@ Subdirectories are:
 
 To run the workflow:
 
 
 To run the workflow:
 

-* cd into cwl directory

 * run the following:
 * 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.  
 
 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 58e38cbf2d6453908bfb5b4c4564daa439996988..9c1e78a86d17e8b74a6422b732160be57feda4c0 100644 (file)
--- 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 
     outputSource: bwamem-gatk-report/gvcf
     format: edam:format_3016 # GVCF
     label: GVCFs generated from GATK 

-    

   report:
     type: File[]  
     outputSource: bwamem-gatk-report/report
   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 (file)
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 c1904f5897fcbb7735ce5991d7934095f64b99a7..7c27a9c6ac9d1baabd92f459364a1b1bbdb9225e 100644 (file)
--- 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
 bam:
   class: File
   location: keep:su92l-4zz18-v4m3dx8agdp1y9r/WGC069888D.bam

+

 sample: WGC069888D
 sample: WGC069888D

diff --git a/WGS-processing/yml/wgs-processing-wf.yml b/WGS-processing/yml/wgs-processing-wf.yml
index 8853a804a7ad036f404a7660b40589eaf0fc2fcf..85b2ffdbbd9b9d62e2611b30e0c29d6c1a1981a9 100644 (file)
--- 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
 reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa