reorg of yml files

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

diff --git a/WGS-processing/yml/annotate-vcf.yml b/WGS-processing/yml/helper/annotate-vcf.yml
similarity index 100%
rename from WGS-processing/yml/annotate-vcf.yml
rename to WGS-processing/yml/helper/annotate-vcf.yml

diff --git a/WGS-processing/yml/bwamem-gatk-report-wf.yml b/WGS-processing/yml/helper/bwamem-gatk-report-wf.yml
similarity index 100%
rename from WGS-processing/yml/bwamem-gatk-report-wf.yml
rename to WGS-processing/yml/helper/bwamem-gatk-report-wf.yml

diff --git a/WGS-processing/yml/bwamem-samtools-sort.yml b/WGS-processing/yml/helper/bwamem-samtools-sort.yml
similarity index 100%
rename from WGS-processing/yml/bwamem-samtools-sort.yml
rename to WGS-processing/yml/helper/bwamem-samtools-sort.yml

diff --git a/WGS-processing/yml/bwamem-samtools-view.yml b/WGS-processing/yml/helper/bwamem-samtools-view.yml
similarity index 100%
rename from WGS-processing/yml/bwamem-samtools-view.yml
rename to WGS-processing/yml/helper/bwamem-samtools-view.yml

diff --git a/WGS-processing/yml/fastqc.yml b/WGS-processing/yml/helper/fastqc.yml
similarity index 100%
rename from WGS-processing/yml/fastqc.yml
rename to WGS-processing/yml/helper/fastqc.yml

diff --git a/WGS-processing/yml/gather-vcf.yml b/WGS-processing/yml/helper/gather-vcf.yml
similarity index 100%
rename from WGS-processing/yml/gather-vcf.yml
rename to WGS-processing/yml/helper/gather-vcf.yml

diff --git a/WGS-processing/yml/gatk-applyBQSR.yml b/WGS-processing/yml/helper/gatk-applyBQSR.yml
similarity index 100%
rename from WGS-processing/yml/gatk-applyBQSR.yml
rename to WGS-processing/yml/helper/gatk-applyBQSR.yml

diff --git a/WGS-processing/yml/gatk-baserecalibrator.yml b/WGS-processing/yml/helper/gatk-baserecalibrator.yml
similarity index 100%
rename from WGS-processing/yml/gatk-baserecalibrator.yml
rename to WGS-processing/yml/helper/gatk-baserecalibrator.yml

diff --git a/WGS-processing/yml/gatk-haplotypecaller-with-interval.yml b/WGS-processing/yml/helper/gatk-haplotypecaller-with-interval.yml
similarity index 100%
rename from WGS-processing/yml/gatk-haplotypecaller-with-interval.yml
rename to WGS-processing/yml/helper/gatk-haplotypecaller-with-interval.yml

diff --git a/WGS-processing/yml/gatk-haplotypecaller.yml b/WGS-processing/yml/helper/gatk-haplotypecaller.yml
similarity index 100%
rename from WGS-processing/yml/gatk-haplotypecaller.yml
rename to WGS-processing/yml/helper/gatk-haplotypecaller.yml

diff --git a/WGS-processing/yml/gatk-selectvariants.yml b/WGS-processing/yml/helper/gatk-selectvariants.yml
similarity index 100%
rename from WGS-processing/yml/gatk-selectvariants.yml
rename to WGS-processing/yml/helper/gatk-selectvariants.yml

diff --git a/WGS-processing/yml/gatk-splitintervals.yml b/WGS-processing/yml/helper/gatk-splitintervals.yml
similarity index 100%
rename from WGS-processing/yml/gatk-splitintervals.yml
rename to WGS-processing/yml/helper/gatk-splitintervals.yml

diff --git a/WGS-processing/yml/gatk-wf-with-interval.yml b/WGS-processing/yml/helper/gatk-wf-with-interval.yml
similarity index 100%
rename from WGS-processing/yml/gatk-wf-with-interval.yml
rename to WGS-processing/yml/helper/gatk-wf-with-interval.yml

diff --git a/WGS-processing/yml/generate-report.yml b/WGS-processing/yml/helper/generate-report.yml
similarity index 100%
rename from WGS-processing/yml/generate-report.yml
rename to WGS-processing/yml/helper/generate-report.yml

diff --git a/WGS-processing/yml/getfastq.yml b/WGS-processing/yml/helper/getfastq.yml
similarity index 100%
rename from WGS-processing/yml/getfastq.yml
rename to WGS-processing/yml/helper/getfastq.yml

diff --git a/WGS-processing/yml/getgvcfs.yml b/WGS-processing/yml/helper/getgvcfs.yml
similarity index 100%
rename from WGS-processing/yml/getgvcfs.yml
rename to WGS-processing/yml/helper/getgvcfs.yml

diff --git a/WGS-processing/yml/gvcf-to-vcf.yml b/WGS-processing/yml/helper/gvcf-to-vcf.yml
similarity index 100%
rename from WGS-processing/yml/gvcf-to-vcf.yml
rename to WGS-processing/yml/helper/gvcf-to-vcf.yml

diff --git a/WGS-processing/yml/mark-duplicates.yml b/WGS-processing/yml/helper/mark-duplicates.yml
similarity index 100%
rename from WGS-processing/yml/mark-duplicates.yml
rename to WGS-processing/yml/helper/mark-duplicates.yml

diff --git a/WGS-processing/yml/report-wf.yml b/WGS-processing/yml/helper/report-wf.yml
similarity index 100%
rename from WGS-processing/yml/report-wf.yml
rename to WGS-processing/yml/helper/report-wf.yml

diff --git a/WGS-processing/yml/samtools-index.yml b/WGS-processing/yml/helper/samtools-index.yml
similarity index 100%
rename from WGS-processing/yml/samtools-index.yml
rename to WGS-processing/yml/helper/samtools-index.yml

diff --git a/WGS-processing/yml/samtools-sort.yml b/WGS-processing/yml/helper/samtools-sort.yml
similarity index 100%
rename from WGS-processing/yml/samtools-sort.yml
rename to WGS-processing/yml/helper/samtools-sort.yml

diff --git a/WGS-processing/yml/scatter-gatk-wf-with-interval.yml b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
similarity index 100%
rename from WGS-processing/yml/scatter-gatk-wf-with-interval.yml
rename to WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml

diff --git a/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC071838D.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC071838D.yml
deleted file mode 100644 (file)
index c1aa1c7..0000000
--- a/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC071838D.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-sample: WGC071838D
-reference:
-  class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
-fastq1:
-  class: File
-  location: keep:su92l-4zz18-9wi0scyveespepp/WGC071838D_R1.fastq.gz
-fastq2:
-  class: File
-  location: keep:su92l-4zz18-9wi0scyveespepp/WGC071838D_R2.fastq.gz
-

diff --git a/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC074701D.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC074701D.yml
deleted file mode 100644 (file)
index 3e45c27..0000000
--- a/WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC074701D.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-sample: WGC074701D
-reference:
-  class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
-fastq1:
-  class: File
-  location: keep:su92l-4zz18-bpfmvsf9wedbefr/WGC074701D_R1.fastq.gz
-fastq2:
-  class: File
-  location: keep:su92l-4zz18-bpfmvsf9wedbefr/WGC074701D_R1.fastq.gz
-

diff --git a/WGS-processing/yml/not-in-use/bwa-gatk-wf-chr19.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-chr19.yml
deleted file mode 100644 (file)
index c46b835..0000000
--- a/WGS-processing/yml/not-in-use/bwa-gatk-wf-chr19.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-sample: hu297A5D_AE2CH6SK4DG
-
-reference:
-  class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
-
-fastq1:
-  class: File
-  location: keep:fafa02df612fe883b6d7bdc0bc755afb+612/hu297A5D_AE2CH6SK4DG-EXT_R1.fastq.gz
-
-fastq2:
-  class: File
-  location: keep:fafa02df612fe883b6d7bdc0bc755afb+612/hu297A5D_AE2CH6SK4DG-EXT_R2.fastq.gz
-

diff --git a/WGS-processing/yml/not-in-use/bwa-gatk-wf-report.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf-report.yml
deleted file mode 100644 (file)
index 7889a82..0000000
--- a/WGS-processing/yml/not-in-use/bwa-gatk-wf-report.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-sample: WGC071838D
-
-reference:
-  class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
-
-fastq1:
-  class: File
-  location: keep:24df1ea93ad5275aa511462ea85b0548+20283/WGC071838D_R1.fastq.gz
-
-fastq2:
-  class: File
-  location: keep:24df1ea93ad5275aa511462ea85b0548+20283/WGC071838D_R2.fastq.gz
-
-clinvarvcf:
-  class: File
-  location: keep:242ba3b9049aee86ab2c72db4f3b2822+223/38/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/WGS-processing/yml/not-in-use/bwa-gatk-wf.yml b/WGS-processing/yml/not-in-use/bwa-gatk-wf.yml
deleted file mode 100644 (file)
index e6bab2f..0000000
--- a/WGS-processing/yml/not-in-use/bwa-gatk-wf.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-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
-