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WGS Processing tutorial updates #1

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84517a7
Update package install instructions for building containers.
ZoeCMa Mar 18, 2025
b689da4
python3 compatibility for the report generator script.
ZoeCMa Mar 18, 2025
3221b02
Update CWL tool definitions for WGS tutorial.
ZoeCMa Mar 18, 2025
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6 changes: 3 additions & 3 deletions WGS-processing/cwl/helper/bwamem-samtools-view.cwl
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Expand Up @@ -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" ]
Expand Down Expand Up @@ -58,7 +58,7 @@ outputs:
glob: "*bam"

arguments:
- /bwa-0.7.17/bwa
- /bwa-0.7.18/bwa
- mem
- -M
- -t
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2 changes: 1 addition & 1 deletion WGS-processing/cwl/helper/generate-report.cwl
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Expand Up @@ -38,7 +38,7 @@ outputs:
outputBinding:
glob: "*html"

baseCommand: python
baseCommand: /usr/bin/python3

arguments:
- $(inputs.reportfunc)
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8 changes: 4 additions & 4 deletions WGS-processing/docker/bwa_samtools/Dockerfile
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Expand Up @@ -3,7 +3,7 @@ USER root
MAINTAINER Sarah Wait Zaranek <swz@curii.com>

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
Expand All @@ -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
4 changes: 2 additions & 2 deletions WGS-processing/docker/clinvar-report/Dockerfile
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Expand Up @@ -4,7 +4,7 @@ MAINTAINER Sarah Wait Zaranek <swz@curii.com>

# 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
Expand All @@ -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
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11 changes: 5 additions & 6 deletions WGS-processing/src/annotation/generatereport.py
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Expand Up @@ -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('&lt;','<')
html_str_encoded = html_str_encoded.replace('&gt;','>')
html_str_encoded = html_str_encoded.replace('_',' ')
section_html = labelhtml+html_str_encoded
html_str = html_str.replace('&lt;','<')
html_str = html_str.replace('&gt;','>')
html_str = html_str.replace('_',' ')
section_html = labelhtml+html_str
return section_html

def generatereport():
Expand Down Expand Up @@ -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()

Expand Down