Rearranging for clarity

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

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

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

diff --git a/cwl/helper/bwa-gatk-wf.cwl b/WGS-processing/cwl/helper/bwa-gatk-wf.cwl
similarity index 100%
rename from cwl/helper/bwa-gatk-wf.cwl
rename to WGS-processing/cwl/helper/bwa-gatk-wf.cwl

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

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

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

diff --git a/cwl/helper/gather-vcf-try2.cwl b/WGS-processing/cwl/helper/gather-vcf-try2.cwl
similarity index 100%
rename from cwl/helper/gather-vcf-try2.cwl
rename to WGS-processing/cwl/helper/gather-vcf-try2.cwl

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

diff --git a/cwl/helper/not-in-use/bwa-gatk-wf.cwl b/WGS-processing/cwl/helper/not-in-use/bwa-gatk-wf.cwl
similarity index 100%
rename from cwl/helper/not-in-use/bwa-gatk-wf.cwl
rename to WGS-processing/cwl/helper/not-in-use/bwa-gatk-wf.cwl

diff --git a/cwl/helper/not-in-use/bwamem-samtools-sort.cwl b/WGS-processing/cwl/helper/not-in-use/bwamem-samtools-sort.cwl
similarity index 100%
rename from cwl/helper/not-in-use/bwamem-samtools-sort.cwl
rename to WGS-processing/cwl/helper/not-in-use/bwamem-samtools-sort.cwl

diff --git a/cwl/helper/not-in-use/calc-coverage.cwl b/WGS-processing/cwl/helper/not-in-use/calc-coverage.cwl
similarity index 100%
rename from cwl/helper/not-in-use/calc-coverage.cwl
rename to WGS-processing/cwl/helper/not-in-use/calc-coverage.cwl

diff --git a/cwl/helper/not-in-use/check-sam.cwl b/WGS-processing/cwl/helper/not-in-use/check-sam.cwl
similarity index 100%
rename from cwl/helper/not-in-use/check-sam.cwl
rename to WGS-processing/cwl/helper/not-in-use/check-sam.cwl

diff --git a/cwl/helper/not-in-use/fix-groups.cwl b/WGS-processing/cwl/helper/not-in-use/fix-groups.cwl
similarity index 100%
rename from cwl/helper/not-in-use/fix-groups.cwl
rename to WGS-processing/cwl/helper/not-in-use/fix-groups.cwl

diff --git a/cwl/helper/not-in-use/samtools-fixmate.cwl b/WGS-processing/cwl/helper/not-in-use/samtools-fixmate.cwl
similarity index 100%
rename from cwl/helper/not-in-use/samtools-fixmate.cwl
rename to WGS-processing/cwl/helper/not-in-use/samtools-fixmate.cwl

diff --git a/cwl/helper/not-in-use/samtools-sort.cwl b/WGS-processing/cwl/helper/not-in-use/samtools-sort.cwl
similarity index 100%
rename from cwl/helper/not-in-use/samtools-sort.cwl
rename to WGS-processing/cwl/helper/not-in-use/samtools-sort.cwl

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

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

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

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

diff --git a/docker/bwa/Dockerfile b/WGS-processing/docker/bwa/Dockerfile
similarity index 100%
rename from docker/bwa/Dockerfile
rename to WGS-processing/docker/bwa/Dockerfile

diff --git a/docker/clinvar-report/Dockerfile b/WGS-processing/docker/clinvar-report/Dockerfile
similarity index 100%
rename from docker/clinvar-report/Dockerfile
rename to WGS-processing/docker/clinvar-report/Dockerfile

diff --git a/docker/fastqc/Dockerfile b/WGS-processing/docker/fastqc/Dockerfile
similarity index 100%
rename from docker/fastqc/Dockerfile
rename to WGS-processing/docker/fastqc/Dockerfile

diff --git a/src/annotation/generatereport.py b/WGS-processing/src/annotation/generatereport.py
similarity index 100%
rename from src/annotation/generatereport.py
rename to WGS-processing/src/annotation/generatereport.py

diff --git a/src/annotation/head.html b/WGS-processing/src/annotation/head.html
similarity index 100%
rename from src/annotation/head.html
rename to WGS-processing/src/annotation/head.html

diff --git a/src/annotation/runcommand b/WGS-processing/src/annotation/runcommand
similarity index 100%
rename from src/annotation/runcommand
rename to WGS-processing/src/annotation/runcommand

diff --git a/src/annotation/sample.html b/WGS-processing/src/annotation/sample.html
similarity index 100%
rename from src/annotation/sample.html
rename to WGS-processing/src/annotation/sample.html

diff --git a/src/annotation/samplelist b/WGS-processing/src/annotation/samplelist
similarity index 100%
rename from src/annotation/samplelist
rename to WGS-processing/src/annotation/samplelist

diff --git a/src/annotation/tail.html b/WGS-processing/src/annotation/tail.html
similarity index 100%
rename from src/annotation/tail.html
rename to WGS-processing/src/annotation/tail.html

diff --git a/src/annotation/test.html b/WGS-processing/src/annotation/test.html
similarity index 100%
rename from src/annotation/test.html
rename to WGS-processing/src/annotation/test.html

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

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

diff --git a/yml/bwa-gatk-wf-WGC071838D.yml b/WGS-processing/yml/bwa-gatk-wf-WGC071838D.yml
similarity index 100%
rename from yml/bwa-gatk-wf-WGC071838D.yml
rename to WGS-processing/yml/bwa-gatk-wf-WGC071838D.yml

diff --git a/yml/bwa-gatk-wf-WGC074701D.yml b/WGS-processing/yml/bwa-gatk-wf-WGC074701D.yml
similarity index 100%
rename from yml/bwa-gatk-wf-WGC074701D.yml
rename to WGS-processing/yml/bwa-gatk-wf-WGC074701D.yml

diff --git a/yml/bwa-gatk-wf-chr19.yml b/WGS-processing/yml/bwa-gatk-wf-chr19.yml
similarity index 100%
rename from yml/bwa-gatk-wf-chr19.yml
rename to WGS-processing/yml/bwa-gatk-wf-chr19.yml

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

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

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

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

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

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

diff --git a/yml/gather-vcf2.yml b/WGS-processing/yml/gather-vcf2.yml
similarity index 100%
rename from yml/gather-vcf2.yml
rename to WGS-processing/yml/gather-vcf2.yml

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

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

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

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

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

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

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

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

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

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

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

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

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

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

diff --git a/yml/samtools-sort-WGC069888D.yml b/WGS-processing/yml/samtools-sort-WGC069888D.yml
similarity index 100%
rename from yml/samtools-sort-WGC069888D.yml
rename to WGS-processing/yml/samtools-sort-WGC069888D.yml

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

diff --git a/docker/bam2fastq/Dockerfile b/docker/bam2fastq/Dockerfile
deleted file mode 100644 (file)
index d40b3fa..0000000
--- a/docker/bam2fastq/Dockerfile
+++ /dev/null
@@ -1,67 +0,0 @@
-FROM arvados/jobs:latest
-USER root
-
-# Install python tools
-RUN apt-get update && apt-get install -y --no-install-recommends apt-utils
-RUN apt-get install -y apt-utils && apt-get install -y unzip
-RUN apt-get install autoconf -y
-RUN apt-get install wget -y
-RUN apt-get install python-pip -y
-RUN apt-get install python-numpy -y && apt-get install python-scipy -y
-RUN apt-get install python-matplotlib -y && apt-get install python-pandas -y
-RUN apt-get upgrade -y
-RUN apt-get clean
-
-# install lib files to build SAMtools
-RUN apt-get install libncurses5-dev -y && apt-get install libbz2-dev -y && apt-get install liblzma-dev -y && apt-get install git -y && apt-get install autoconf -y
-
-# installing zlib1g
-RUN apt-get install zlib1g-dev -y
-RUN apt-get install zlib1g -y
-
-# Installing xz-utils
-
-RUN apt-get install xz-utils -y
-
-# Installing liblzma-dev
-RUN apt-get install liblzma-dev -y
-
-# Installing pthreads
-RUN apt-get install libpthread-stubs0-dev -y
-
-# Installing libcurl
-RUN apt-get install libcurl3-openssl-dev -y
-
-# Installing libcrypto
-RUN apt-get install libssl-dev -y
-
-# Installing bc
-RUN apt-get install bc -y
-
-# installing build essentials
-RUN apt-get install build-essential -y
-
-# Installing parallel
-RUN apt-get install parallel -y
-
-# Installing Cmake
-RUN apt-get install cmake -y
-
-# Installing SDSL
-RUN cd /tmp && git clone 'https://github.com/simongog/sdsl-lite.git' && cd sdsl-lite && ./install.sh /usr/local
-
-RUN apt-get remove libhts-dev
-
-# Installing htslib
-RUN cd /tmp && wget http://github.com/samtools/htslib/archive/1.10.2.zip && unzip 1.10.2 && cd htslib-1.10.2 && make && make install && cd /tmp && rm -rf htslib-1.10.2 && ldconfig
-
-# Installing samtools
-
-RUN wget http://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && tar -xvf samtools-1.10.tar.bz2 && cd samtools-1.10 && autoheader && autoconf && ./configure && make && make install 
-
-RUN git clone --recursive https://github.com/jts/bam2fastq
-WORKDIR /bam2fastq
-RUN make
-
-WORKDIR /
-