diff --git a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl index 71fd365..ea12a55 100644 --- a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl +++ b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl @@ -12,12 +12,12 @@ hints: outputDirType: keep_output_dir ResourceRequirement: ramMin: 30000 - coresMin: 16 + coresMin: 6 SoftwareRequirement: packages: BWA: specs: [ "https://identifiers.org/rrid/RRID:SCR_010910" ] - version: [ "0.7.17" ] + version: [ "0.7.18" ] Samtools: specs: [ "https://identifiers.org/rrid/RRID:SCR_002105" ] version: [ "1.10" ] @@ -58,7 +58,7 @@ outputs: glob: "*bam" arguments: - - /bwa-0.7.17/bwa + - /bwa-0.7.18/bwa - mem - -M - -t diff --git a/WGS-processing/cwl/helper/generate-report.cwl b/WGS-processing/cwl/helper/generate-report.cwl index 3773f7d..a0b86bb 100644 --- a/WGS-processing/cwl/helper/generate-report.cwl +++ b/WGS-processing/cwl/helper/generate-report.cwl @@ -38,7 +38,7 @@ outputs: outputBinding: glob: "*html" -baseCommand: python +baseCommand: /usr/bin/python3 arguments: - $(inputs.reportfunc) diff --git a/WGS-processing/docker/bwa_samtools/Dockerfile b/WGS-processing/docker/bwa_samtools/Dockerfile index 5f01b1d..14bfd75 100644 --- a/WGS-processing/docker/bwa_samtools/Dockerfile +++ b/WGS-processing/docker/bwa_samtools/Dockerfile @@ -3,7 +3,7 @@ USER root MAINTAINER Sarah Wait Zaranek RUN apt-get update -qy -RUN apt-get install -qy build-essential wget cmake zlib1g-dev python-pip unzip libbz2-dev liblzma-dev libcurl4-openssl-dev libncurses-dev autoconf git +RUN apt-get install -qy build-essential wget cmake zlib1g-dev python3-pip unzip libbz2-dev liblzma-dev libcurl4-openssl-dev libncurses-dev autoconf git RUN mkdir -p /usr/share/man/man1 RUN apt-get install -qy default-jdk @@ -13,12 +13,12 @@ RUN cd /tmp && git clone 'https://github.com/simongog/sdsl-lite.git' && cd sdsl- RUN apt-get remove libhts-dev # Install htslib 1.10.2 -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 +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 && /sbin/ldconfig # Install samtools 1.10 RUN wget https://github.com/samtools/samtools/archive/1.10.zip && unzip 1.10 && cd samtools-1.10 && autoheader && autoconf && ./configure && make && make install -# Install BWA 07.7.17 -RUN wget https://github.com/lh3/bwa/archive/v0.7.17.zip && unzip v0.7.17 && cd bwa-0.7.17 && make +# Install BWA 07.7.18 +RUN wget https://github.com/lh3/bwa/archive/v0.7.18.zip && unzip v0.7.18 && cd bwa-0.7.18 && make CMD /bin/sh diff --git a/WGS-processing/docker/clinvar-report/Dockerfile b/WGS-processing/docker/clinvar-report/Dockerfile index 2c0976b..32729c0 100644 --- a/WGS-processing/docker/clinvar-report/Dockerfile +++ b/WGS-processing/docker/clinvar-report/Dockerfile @@ -4,7 +4,7 @@ MAINTAINER Sarah Wait Zaranek # Install python tools RUN apt-get update && apt-get install -y --no-install-recommends apt-utils -RUN apt-get install -qy apt-utils unzip autoconf wget python-pip python-numpy python-scipy python-matplotlib python-pandas +RUN apt-get install -qy apt-utils unzip autoconf wget python3-pip python3-numpy python3-scipy python3-matplotlib python3-pandas RUN apt-get upgrade -y RUN apt-get clean @@ -18,7 +18,7 @@ RUN cd /tmp && git clone 'https://github.com/simongog/sdsl-lite.git' && cd sdsl- RUN apt-get remove libhts-dev # Install htslib 1.10.2 -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 +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 && /sbin/ldconfig # Install bcftools 1.10.2 RUN wget http://github.com/samtools/bcftools/archive/1.10.2.zip && unzip 1.10.2 && cd bcftools-1.10.2 && autoheader && autoconf && ./configure && make && make install diff --git a/WGS-processing/src/annotation/generatereport.py b/WGS-processing/src/annotation/generatereport.py index d07ec93..46921d9 100644 --- a/WGS-processing/src/annotation/generatereport.py +++ b/WGS-processing/src/annotation/generatereport.py @@ -13,11 +13,10 @@ def tablegeneration(reportdata,sectionlabel): str_io = io.StringIO() reportdatasub.to_html(buf=str_io, classes='table table-bordered',index_names=False,index=False) html_str = str_io.getvalue() - html_str_encoded = unicode(html_str).encode('utf8') - html_str_encoded = html_str_encoded.replace('<','<') - html_str_encoded = html_str_encoded.replace('>','>') - html_str_encoded = html_str_encoded.replace('_',' ') - section_html = labelhtml+html_str_encoded + html_str = html_str.replace('<','<') + html_str = html_str.replace('>','>') + html_str = html_str.replace('_',' ') + section_html = labelhtml+html_str return section_html def generatereport(): @@ -90,7 +89,7 @@ def generatereport(): total_html = source_code_head + pathogenic_html + likely_pathogenic_html + drug_html + protective_html + risk_html + affects_html + association_html + other_html + benign_html + likely_benign_html + source_code_tail # write out report html - f = open(samplename+'.html','wb') + f = open(samplename+'.html','w') f.write(total_html) f.close()