From f46aac417fb5b8b3d3db810b9a62e94571765f77 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Thu, 25 Jun 2020 13:06:46 +0000 Subject: [PATCH] reorg of yml files Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- .../yml/{ => helper}/annotate-vcf.yml | 0 .../{ => helper}/bwamem-gatk-report-wf.yml | 0 .../yml/{ => helper}/bwamem-samtools-sort.yml | 0 .../yml/{ => helper}/bwamem-samtools-view.yml | 0 WGS-processing/yml/{ => helper}/fastqc.yml | 0 .../yml/{ => helper}/gather-vcf.yml | 0 .../yml/{ => helper}/gatk-applyBQSR.yml | 0 .../{ => helper}/gatk-baserecalibrator.yml | 0 .../gatk-haplotypecaller-with-interval.yml | 0 .../yml/{ => helper}/gatk-haplotypecaller.yml | 0 .../yml/{ => helper}/gatk-selectvariants.yml | 0 .../yml/{ => helper}/gatk-splitintervals.yml | 0 .../{ => helper}/gatk-wf-with-interval.yml | 0 .../yml/{ => helper}/generate-report.yml | 0 WGS-processing/yml/{ => helper}/getfastq.yml | 0 WGS-processing/yml/{ => helper}/getgvcfs.yml | 0 .../yml/{ => helper}/gvcf-to-vcf.yml | 0 .../yml/{ => helper}/mark-duplicates.yml | 0 WGS-processing/yml/{ => helper}/report-wf.yml | 0 .../yml/{ => helper}/samtools-index.yml | 0 .../yml/{ => helper}/samtools-sort.yml | 0 .../scatter-gatk-wf-with-interval.yml | 0 .../yml/not-in-use/bwa-gatk-wf-WGC071838D.yml | 11 ------- .../yml/not-in-use/bwa-gatk-wf-WGC074701D.yml | 11 ------- .../yml/not-in-use/bwa-gatk-wf-chr19.yml | 14 --------- .../yml/not-in-use/bwa-gatk-wf-report.yml | 29 ------------------- WGS-processing/yml/not-in-use/bwa-gatk-wf.yml | 11 ------- 27 files changed, 76 deletions(-) rename WGS-processing/yml/{ => helper}/annotate-vcf.yml (100%) rename WGS-processing/yml/{ => helper}/bwamem-gatk-report-wf.yml (100%) rename WGS-processing/yml/{ => helper}/bwamem-samtools-sort.yml (100%) rename WGS-processing/yml/{ => helper}/bwamem-samtools-view.yml (100%) rename WGS-processing/yml/{ => helper}/fastqc.yml (100%) rename WGS-processing/yml/{ => helper}/gather-vcf.yml (100%) rename WGS-processing/yml/{ => helper}/gatk-applyBQSR.yml (100%) rename WGS-processing/yml/{ => helper}/gatk-baserecalibrator.yml (100%) rename WGS-processing/yml/{ => helper}/gatk-haplotypecaller-with-interval.yml (100%) rename WGS-processing/yml/{ => helper}/gatk-haplotypecaller.yml (100%) rename WGS-processing/yml/{ => helper}/gatk-selectvariants.yml (100%) rename WGS-processing/yml/{ => helper}/gatk-splitintervals.yml (100%) rename WGS-processing/yml/{ => helper}/gatk-wf-with-interval.yml (100%) rename WGS-processing/yml/{ => helper}/generate-report.yml (100%) rename WGS-processing/yml/{ => helper}/getfastq.yml (100%) rename WGS-processing/yml/{ => helper}/getgvcfs.yml (100%) rename WGS-processing/yml/{ => helper}/gvcf-to-vcf.yml (100%) rename WGS-processing/yml/{ => helper}/mark-duplicates.yml (100%) rename WGS-processing/yml/{ => helper}/report-wf.yml (100%) rename WGS-processing/yml/{ => helper}/samtools-index.yml (100%) rename WGS-processing/yml/{ => helper}/samtools-sort.yml (100%) rename WGS-processing/yml/{ => helper}/scatter-gatk-wf-with-interval.yml (100%) delete mode 100644 WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC071838D.yml delete mode 100644 WGS-processing/yml/not-in-use/bwa-gatk-wf-WGC074701D.yml delete mode 100644 WGS-processing/yml/not-in-use/bwa-gatk-wf-chr19.yml delete mode 100644 WGS-processing/yml/not-in-use/bwa-gatk-wf-report.yml delete mode 100644 WGS-processing/yml/not-in-use/bwa-gatk-wf.yml 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 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 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 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 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 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 - -- 2.30.2