User configurable hardware resources

Merge request

Please fill in the checklist below and comment as needed.

• Was code modified? Briefly describe. See below
• Was documentation modified? Briefly describe.
• Is this a bug-fix? Briefly describe. Yes. See below
• Is this a feature addition? Briefly describe. Yes. See below
• Did you modify QuaC-Watch config file? If so, did you modify multiqc template configs/multiqc_config_template.jinja2 and script src/quac_watch/create_mutliqc_configs.py as necessary? No
• Did you perform system-level testing manually as described in master readme doc? Did it pass completely? If not why?
• Updated Changelog.md file with change logs in recommended format?

Anything else reviewer should know?

• Previously hardcoded hardware resources for snakemake rules can now be supplied via configs/workflow.yaml (closes #48 (closed))
• Modified multiqc conda env config to use explicit dependencies to get around installation issues (closes #47 (closed))

configs/env/multiqc.yaml

@@ -3,5 +3,82 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python =3.6
-  - multiqc ==1.9
+  - python=3.6.13
+  - multiqc==1.9
+  - networkx=2.5
+  - numpy=1.19.5
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - brotlipy=0.7.0
+  - ca-certificates=2021.5.30
+  - certifi=2021.5.30
+  - cffi=1.14.6
+  - chardet=4.0.0
+  - charset-normalizer=2.0.0
+  - click=8.0.1
+  - coloredlogs=15.0.1
+  - colormath=3.0.0
+  - cryptography=3.4.7
+  - cycler=0.10.0
+  - decorator=5.0.9
+  - freetype=2.10.4
+  - future=0.18.2
+  - humanfriendly=9.2
+  - idna=3.1
+  - importlib-metadata=4.6.3
+  - jbig=2.1
+  - jinja2=3.0.1
+  - jpeg=9d
+  - kiwisolver=1.3.1
+  - lcms2=2.12
+  - ld_impl_linux-64=2.36.1
+  - lerc=2.2.1
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libdeflate=1.7
+  - libffi=3.3
+  - libgcc-ng=11.1.0
+  - libgfortran-ng=11.1.0
+  - libgfortran5=11.1.0
+  - libgomp=11.1.0
+  - liblapack=3.9.0
+  - libopenblas=0.3.17
+  - libpng=1.6.37
+  - libstdcxx-ng=11.1.0
+  - libtiff=4.3.0
+  - libwebp-base=1.2.0
+  - lz4-c=1.9.3
+  - lzstring=1.0.4
+  - markdown=3.3.4
+  - markupsafe=2.0.1
+  - matplotlib-base=3.3.4
+  - ncurses=6.2
+  - olefile=0.46
+  - openjpeg=2.4.0
+  - openssl=1.1.1k
+  - pillow=8.3.1
+  - pip=21.2.3
+  - pycparser=2.20
+  - pyopenssl=20.0.1
+  - pyparsing=2.4.7
+  - pysocks=1.7.1
+  - python-dateutil=2.8.2
+  - python_abi=3.6
+  - pyyaml=5.4.1
+  - readline=8.1
+  - requests=2.26.0
+  - setuptools=49.6.0
+  - simplejson=3.8.1
+  - six=1.16.0
+  - spectra=0.0.11
+  - sqlite=3.36.0
+  - tk=8.6.10
+  - tornado=6.1
+  - typing_extensions=3.10.0.0
+  - urllib3=1.26.6
+  - wheel=0.37.0
+  - xz=5.2.5
+  - yaml=0.2.5
+  - zipp=3.5.0
+  - zlib=1.2.11
+  - zstd=1.5.0