Updating yml

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

diff --git a/yml/annotate-vcf.yml b/yml/annotate-vcf.yml
new file mode 100644 (file)
index 0000000..74f0856
--- /dev/null
+++ b/yml/annotate-vcf.yml
@@ -0,0 +1,7 @@
+vcf:
+  class: File
+  location: keep:542f0989c5ee117e20d293ef82311192+114145/hu34D5B9_var-GS000015891-ASM.vcf.gz 
+
+clinvarvcf:
+  class: File
+  location: keep:80aadf801bccd1e1d838b07d46d4de63+1712/37/clinvar.vcf.gz

diff --git a/yml/bwa-gatk-wf-chr19.yml b/yml/bwa-gatk-wf-chr19.yml
index 0844fec4add23ad87270cec1dfb9bea8c86b607f..c46b835c1a45350297a928e43fffa3fbe8f0de3a 100644 (file)
--- a/yml/bwa-gatk-wf-chr19.yml
+++ b/yml/bwa-gatk-wf-chr19.yml
@@ -1,11 +1,14 @@
 sample: hu297A5D_AE2CH6SK4DG
 sample: hu297A5D_AE2CH6SK4DG

+

 reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa

+

 fastq1:
   class: File
 fastq1:
   class: File

-  location: ../../bam/hu297A5D_AE2CH6SK4DG-EXT_R1.fastq.gz
+  location: keep:fafa02df612fe883b6d7bdc0bc755afb+612/hu297A5D_AE2CH6SK4DG-EXT_R1.fastq.gz
+

 fastq2:
   class: File
 fastq2:
   class: File

-  location: ../../bam/hu297A5D_AE2CH6SK4DG-EXT_R2.fastq.gz
+  location: keep:fafa02df612fe883b6d7bdc0bc755afb+612/hu297A5D_AE2CH6SK4DG-EXT_R2.fastq.gz

 
 

diff --git a/yml/bwa-gatk-wf-report.yml b/yml/bwa-gatk-wf-report.yml
new file mode 100644 (file)
index 0000000..35a0998
--- /dev/null
+++ b/yml/bwa-gatk-wf-report.yml
@@ -0,0 +1,29 @@
+sample: hu297A5D_AE2CH6SK4DG
+
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
+fastq1:
+  class: File
+  location: keep:06a9452462b67765a81352638a610a5a+198/hu297A5D_AE2CH6SK4DG-EXT_100000_R1.fastq.gz
+
+fastq2:
+  class: File
+  location: keep:06a9452462b67765a81352638a610a5a+198/hu297A5D_AE2CH6SK4DG-EXT_100000_R2.fastq.gz
+
+clinvarvcf:
+  class: File
+  location: keep:80aadf801bccd1e1d838b07d46d4de63+1712/38/clinvar.vcf.gz
+
+reportfunc:
+  class: File
+  location: ../src/annotation/generatereport.py
+
+headhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/head.html
+
+tailhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/tail.html

diff --git a/yml/bwa-gatk-wf.yml b/yml/bwa-gatk-wf.yml
index 549033e70547a794adc883370f2ffa8ec7a8a998..e6bab2f0b5c13f739664454adbdf127e01811e1e 100644 (file)
--- a/yml/bwa-gatk-wf.yml
+++ b/yml/bwa-gatk-wf.yml
@@ -4,8 +4,8 @@ reference:
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 fastq1:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 fastq1:
   class: File

-  location: ../../bam/hu297A5D_AE2CH6SK4DG-EXT_100000_R1.fastq.gz
+  location: keep:06a9452462b67765a81352638a610a5a+198/hu297A5D_AE2CH6SK4DG-EXT_100000_R1.fastq.gz

 fastq2:
   class: File
 fastq2:
   class: File

-  location: ../../bam/hu297A5D_AE2CH6SK4DG-EXT_100000_R2.fastq.gz
+  location: keep:06a9452462b67765a81352638a610a5a+198/hu297A5D_AE2CH6SK4DG-EXT_100000_R2.fastq.gz

 
 

diff --git a/yml/generate-report.yml b/yml/generate-report.yml
new file mode 100644 (file)
index 0000000..5fd4293
--- /dev/null
+++ b/yml/generate-report.yml
@@ -0,0 +1,12 @@
+reportfunc:
+  class: File
+  location: ../src/annotation/generatereport.py
+sampletxt:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/hu34D5B9_var-GS000015891-ASM.txt
+headhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/head.html
+tailhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/tail.html

diff --git a/yml/gvcf-to-vcf.yml b/yml/gvcf-to-vcf.yml
new file mode 100644 (file)
index 0000000..270836e
--- /dev/null
+++ b/yml/gvcf-to-vcf.yml
@@ -0,0 +1,5 @@
+gvcf:
+  class: File
+  location: keep:02615a79bbe37b48629db97ab43147ae+1123/hu297A5D_AE2CH6SK4DG.gatk.g.vcf 
+
+samplename: hu297A5D_AE2CH6SK4DG

diff --git a/yml/report-wf.yml b/yml/report-wf.yml
new file mode 100644 (file)
index 0000000..c5e5593
--- /dev/null
+++ b/yml/report-wf.yml
@@ -0,0 +1,21 @@
+gvcf:
+  class: File
+  location: keep:02615a79bbe37b48629db97ab43147ae+1123/hu297A5D_AE2CH6SK4DG.gatk.g.vcf
+
+samplename: hu297A5D_AE2CH6SK4DG
+
+clinvarvcf:
+  class: File
+  location: keep:80aadf801bccd1e1d838b07d46d4de63+1712/38/clinvar.vcf.gz
+
+reportfunc:
+  class: File
+  location: ../src/annotation/generatereport.py
+
+headhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/head.html
+
+tailhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/tail.html