Commit 2bfcd999 authored by Sander Bollen's avatar Sander Bollen
Browse files

add final multiqc report

parent 818cff1f
......@@ -560,3 +560,17 @@ rule merge_stats:
stats=out_path("stats.json")
conda: "envs/collectstats.yml"
shell: "python {input.mpy} --vcfstats {input.vstat} {input.cols} > {output.stats}"
rule multiqc:
"""
Create multiQC report
Depends on stats.json to forcefully run at end of pipeline
"""
input:
stats=out_path("stats.json")
params:
odir=out_path(".")
output:
report=out_path("multiqc_report/multiqc_report.html")
shell: "multiqc -o {output.report} {params.odir}"
name: hutspot-multiqc
channels:
- bioconda
- conda-forge
- defaults
- r
dependencies:
- multiqc=1.5=py36_0
- simplejson=3.8.1=py36_0
- asn1crypto=0.24.0=py36_0
- backports=1.0=py36_1
- backports.functools_lru_cache=1.5=py36_0
- ca-certificates=2018.1.18=0
- certifi=2018.1.18=py36_0
- cffi=1.11.5=py36_0
- chardet=3.0.4=py36_0
- click=6.7=py_1
- colormath=3.0.0=py_2
- cryptography=2.2.1=py36_0
- cycler=0.10.0=py36_0
- dbus=1.10.22=0
- decorator=4.2.1=py36_0
- expat=2.2.5=0
- fontconfig=2.12.1=4
- freetype=2.7=1
- future=0.16.0=py36_0
- gettext=0.19.8.1=0
- glib=2.55.0=0
- gst-plugins-base=1.8.0=0
- gstreamer=1.8.0=1
- icu=58.2=0
- idna=2.6=py36_1
- jinja2=2.10=py36_0
- jpeg=9b=2
- libffi=3.2.1=3
- libiconv=1.15=0
- libpng=1.6.34=0
- libxcb=1.13=0
- libxml2=2.9.8=0
- lzstring=1.0.3=py36_0
- markdown=2.6.11=py_0
- markupsafe=1.0=py36_0
- matplotlib=2.1.0=py36_0
- ncurses=5.9=10
- networkx=2.0=py36_1
- openssl=1.0.2n=0
- pcre=8.41=1
- pip=9.0.1=py36_1
- pycparser=2.18=py36_0
- pyopenssl=17.5.0=py36_0
- pyparsing=2.2.0=py36_0
- pyqt=5.6.0=py36_4
- pysocks=1.6.8=py36_1
- python=3.6.3=1
- python-dateutil=2.7.2=py_0
- pytz=2018.3=py_0
- pyyaml=3.12=py36_1
- qt=5.6.2=3
- readline=6.2=0
- requests=2.18.4=py36_1
- setuptools=39.0.1=py36_0
- sip=4.18=py36_1
- six=1.11.0=py36_1
- spectra=0.0.11=py_0
- sqlite=3.13.0=1
- tk=8.5.19=2
- tornado=5.0.1=py36_1
- urllib3=1.22=py36_0
- wheel=0.30.0=py36_2
- xorg-libxau=1.0.8=3
- xorg-libxdmcp=1.1.2=3
- xz=5.2.3=0
- yaml=0.1.7=0
- zlib=1.2.11=0
- libgcc=5.2.0=0
- mkl=2017.0.3=0
- numpy=1.13.1=py36_0
- pip:
- backports.functools-lru-cache==1.5
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