From cec9a7f6a83fc2596e042e8adc6179b202f92a6e Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Wed, 17 Jun 2020 16:20:39 +0000 Subject: [PATCH] Rearranging for clarity Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- .../cwl}/helper/annotate-vcf.cwl | 0 .../cwl}/helper/bwa-gatk-report-wf.cwl | 0 .../cwl}/helper/bwa-gatk-wf.cwl | 0 .../cwl}/helper/bwamem-samtools-view.cwl | 0 {cwl => WGS-processing/cwl}/helper/fastqc.cwl | 0 .../cwl}/helper/gather-array-vcf.cwl | 0 .../cwl}/helper/gather-vcf-try2.cwl | 0 .../cwl}/helper/gather-vcf.cwl | 0 .../cwl}/helper/gatk-applyBQSR.cwl | 0 .../helper/gatk-applyBSQR-with-interval.cwl | 0 .../gatk-baserecalibrator-with-interval.cwl | 0 .../cwl}/helper/gatk-baserecalibrator.cwl | 0 .../gatk-haplotypecaller-with-interval.cwl | 0 .../cwl}/helper/gatk-haplotypecaller.cwl | 0 .../cwl}/helper/gatk-selectvariants.cwl | 0 .../cwl}/helper/gatk-splitintervals.cwl | 0 .../cwl}/helper/gatk-wf-with-interval.cwl | 0 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.../src}/annotation/test.html | 0 {yml => WGS-processing/yml}/annotate-vcf.yml | 0 .../yml}/bwa-gatk-report-wf-UK.yml | 0 .../yml}/bwa-gatk-wf-WGC071838D.yml | 0 .../yml}/bwa-gatk-wf-WGC074701D.yml | 0 .../yml}/bwa-gatk-wf-chr19.yml | 0 .../yml}/bwa-gatk-wf-report.yml | 0 {yml => WGS-processing/yml}/bwa-gatk-wf.yml | 0 .../yml}/bwamem-samtools-sort.yml | 0 .../yml}/bwamem-samtools-view.yml | 0 {yml => WGS-processing/yml}/check-sam.yml | 0 {yml => WGS-processing/yml}/gather-vcf.yml | 0 {yml => WGS-processing/yml}/gather-vcf2.yml | 0 .../yml}/gatk-applyBQSR.yml | 0 .../yml}/gatk-baserecalibrator.yml | 0 .../gatk-haplotypecaller-with-interval.yml | 0 .../yml}/gatk-haplotypecaller.yml | 0 .../yml}/gatk-selectvariants.yml | 0 .../yml}/gatk-splitintervals.yml | 0 .../yml}/gatk-wf-with-interval.yml | 0 .../yml}/generate-report.yml | 0 {yml => WGS-processing/yml}/getfastq.yml | 0 {yml => WGS-processing/yml}/getgvcfs.yml | 0 {yml => WGS-processing/yml}/gvcf-to-vcf.yml | 0 .../yml}/mark-duplicates.yml | 0 {yml => WGS-processing/yml}/report-wf.yml | 0 .../yml}/samtools-index.yml | 0 .../yml}/samtools-sort-WGC069888D.yml | 0 .../yml}/scatter-gatk-wf-with-interval.yml | 0 docker/bam2fastq/Dockerfile | 67 ------------------- 72 files changed, 67 deletions(-) rename {cwl => WGS-processing/cwl}/helper/annotate-vcf.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/bwa-gatk-report-wf.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/bwa-gatk-wf.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/bwamem-samtools-view.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/fastqc.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/gather-array-vcf.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/gather-vcf-try2.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/gather-vcf.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/gatk-applyBQSR.cwl (100%) rename {cwl => WGS-processing/cwl}/helper/gatk-applyBSQR-with-interval.cwl (100%) rename {cwl => 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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 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 / - -- 2.30.2