Adopt BCCDC-PHL/FluViewer

.github/scripts/download_assemblies.sh

@@ -9,6 +9,6 @@ curl -o .github/data/assemblies/MK583613.1_segment_4_HA_H3N2.fa "https://eutils.
 curl -o .github/data/assemblies/MK583614.1_segment_5_NP_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583614.1&db=nucleotide&rettype=fasta"
 curl -o .github/data/assemblies/MK583615.1_segment_6_NA_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583615.1&db=nucleotide&rettype=fasta"
 
-cat .github/data/assemblies/MK58361*.fa > .github/data/assemblies/MK58361X-H3N2.fa
+cat .github/data/assemblies/MK58361*_segment_*.fa > .github/data/assemblies/MK58361X-H3N2.fa
 
 rm .github/data/assemblies/MK58361*.1_segment_*.fa

.github/scripts/run_pipeline.sh

@@ -15,7 +15,7 @@ if [ -z "${GITHUB_ACTIONS}" ]; then
 else
     echo "In GitHub Actions environment. Modifying nextflow.config and FluViewer.nf."
     sed -i 's/cpus = 8/cpus = 4/g' nextflow.config
-    sed -i '/memory/d' modules/FluViewer.nf
+    sed -i '/memory/d' modules/fluviewer.nf
 fi
 
 nextflow -log artifacts/nextflow.log \

bin/tools.py

@@ -12,7 +12,7 @@ def flex_translate(nt_seq, debug=False):
 		- An integer indicating the best reading frame that was used for translation (0, 1, or 2)
 		- An integer indicating the number of stop codons in this best translation candidate
 	"""
-	min_count = np.Inf
+	min_count = np.inf
 	best_seq = None
 	best_frame = -1
 

environments/environment.yml

@@ -4,263 +4,8 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=2_gnu
-  - _r-mutex=1.0.1=anacondar_1
-  - alsa-lib=1.2.10=hd590300_0
-  - argcomplete=3.1.1=pyhd8ed1ab_0
-  - binutils_impl_linux-64=2.40=hf600244_0
-  - bioconductor-biobase=2.58.0=r42ha9d7317_1
-  - bioconductor-biocgenerics=0.44.0=r42hdfd78af_0
-  - bioconductor-biocio=1.8.0=r42hdfd78af_0
-  - bioconductor-biocparallel=1.32.5=r42hf17093f_1
-  - bioconductor-biostrings=2.66.0=r42ha9d7317_1
-  - bioconductor-data-packages=20230718=hdfd78af_1
-  - bioconductor-delayedarray=0.24.0=r42ha9d7317_1
-  - bioconductor-genomeinfodb=1.34.9=r42hdfd78af_0
-  - bioconductor-genomeinfodbdata=1.2.9=r42hdfd78af_0
-  - bioconductor-genomicalignments=1.34.0=r42ha9d7317_1
-  - bioconductor-genomicranges=1.50.0=r42ha9d7317_1
-  - bioconductor-iranges=2.32.0=r42ha9d7317_1
-  - bioconductor-matrixgenerics=1.10.0=r42hdfd78af_0
-  - bioconductor-noiseq=2.42.0=r42hdfd78af_0
-  - bioconductor-rhtslib=2.0.0=r42ha9d7317_1
-  - bioconductor-rsamtools=2.14.0=r42hf17093f_1
-  - bioconductor-rtracklayer=1.58.0=r42h58c1800_2
-  - bioconductor-s4vectors=0.36.0=r42ha9d7317_1
-  - bioconductor-summarizedexperiment=1.28.0=r42hdfd78af_0
-  - bioconductor-xvector=0.38.0=r42ha9d7317_1
-  - bioconductor-zlibbioc=1.44.0=r42ha9d7317_2
-  - blast=2.14.1=pl5321h6f7f691_0
-  - brotli-bin=1.1.0=hd590300_0
-  - brotli-python=1.1.0=py310hc6cd4ac_0
-  - bwidget=1.9.14=ha770c72_1
-  - bzip2=1.0.8=h7f98852_4
-  - c-ares=1.19.1=hd590300_0
-  - ca-certificates=2024.2.2=hbcca054_0
-  - cairo=1.16.0=h0c91306_1017
-  - certifi=2024.2.2=pyhd8ed1ab_0
-  - charset-normalizer=3.2.0=pyhd8ed1ab_0
-  - click=8.1.7=unix_pyh707e725_0
-  - coloredlogs=15.0.1=pyhd8ed1ab_3
-  - colormath=3.0.0=py_2
-  - curl=8.2.1=hca28451_0
-  - cycler=0.11.0=pyhd8ed1ab_0
-  - entrez-direct=16.2=he881be0_1
-  - et_xmlfile=1.1.0=pyhd8ed1ab_0
-  - expat=2.5.0=hcb278e6_1
-  - fastp=0.23.4=hadf994f_2
-  - fastqc=0.12.1=hdfd78af_0
-  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
-  - font-ttf-inconsolata=3.000=h77eed37_0
-  - font-ttf-source-code-pro=2.038=h77eed37_0
-  - font-ttf-ubuntu=0.83=hab24e00_0
-  - fontconfig=2.14.2=h14ed4e7_0
-  - fonts-conda-ecosystem=1=0
-  - fonts-conda-forge=1=0
-  - freetype=2.12.1=hca18f0e_1
-  - fribidi=1.0.10=h36c2ea0_0
-  - future=0.18.3=pyhd8ed1ab_0
-  - gcc_impl_linux-64=13.2.0=h338b0a0_0
-  - genoflu=1.03=hdfd78af_0
-  - gettext=0.21.1=h27087fc_0
-  - gfortran_impl_linux-64=13.2.0=h76e1118_0
-  - giflib=5.2.1=h0b41bf4_3
-  - graphite2=1.3.13=h58526e2_1001
-  - gsl=2.7=he838d99_0
-  - gxx_impl_linux-64=13.2.0=h338b0a0_0
-  - harfbuzz=8.2.0=h3d44ed6_0
-  - htslib=1.18=h81da01d_0
-  - icu=73.2=h59595ed_0
-  - idna=3.4=pyhd8ed1ab_0
-  - importlib-metadata=6.8.0=pyha770c72_0
-  - isa-l=2.30.0=ha770c72_4
-  - jinja2=3.1.2=pyhd8ed1ab_1
-  - jq=1.6=h36c2ea0_1000
-  - kernel-headers_linux-64=2.6.32=he073ed8_16
-  - keyutils=1.6.1=h166bdaf_0
-  - krb5=1.21.2=h659d440_0
-  - lcms2=2.15=haa2dc70_1
-  - ld_impl_linux-64=2.40=h41732ed_0
-  - lerc=4.0.0=h27087fc_0
-  - libblas=3.9.0=18_linux64_openblas
-  - libbrotlicommon=1.1.0=hd590300_0
-  - libbrotlidec=1.1.0=hd590300_0
-  - libbrotlienc=1.1.0=hd590300_0
-  - libcblas=3.9.0=18_linux64_openblas
-  - libcups=2.3.3=h4637d8d_4
-  - libcurl=8.2.1=hca28451_0
-  - libdeflate=1.18=h0b41bf4_0
-  - libedit=3.1.20191231=he28a2e2_2
-  - libev=4.33=h516909a_1
-  - libexpat=2.5.0=hcb278e6_1
-  - libffi=3.4.2=h7f98852_5
-  - libgcc-devel_linux-64=13.2.0=ha9c7c90_0
-  - libgcc-ng=13.2.0=h807b86a_0
-  - libgfortran-ng=13.2.0=h69a702a_0
-  - libgfortran5=13.2.0=ha4646dd_0
-  - libglib=2.78.0=hebfc3b9_0
-  - libgomp=13.2.0=h807b86a_0
-  - libiconv=1.17=h166bdaf_0
-  - libidn2=2.3.4=h166bdaf_0
-  - libjpeg-turbo=2.1.5.1=h0b41bf4_0
-  - liblapack=3.9.0=18_linux64_openblas
-  - libnghttp2=1.52.0=h61bc06f_0
-  - libnsl=2.0.0=h7f98852_0
-  - libopenblas=0.3.24=pthreads_h413a1c8_0
-  - libpng=1.6.39=h753d276_0
-  - libsanitizer=13.2.0=h7e041cc_0
-  - libsqlite=3.43.0=h2797004_0
-  - libssh2=1.11.0=h0841786_0
-  - libstdcxx-devel_linux-64=13.2.0=ha9c7c90_0
-  - libstdcxx-ng=13.2.0=h7e041cc_0
-  - libtiff=4.5.1=h8b53f26_1
-  - libunistring=0.9.10=h7f98852_0
-  - libuuid=2.38.1=h0b41bf4_0
-  - libwebp-base=1.3.1=hd590300_0
-  - libxcb=1.15=h0b41bf4_0
-  - libxml2=2.11.5=h232c23b_1
-  - libzlib=1.2.13=hd590300_5
-  - lzstring=1.0.4=py_1001
-  - make=4.3=hd18ef5c_1
-  - markdown=3.4.4=pyhd8ed1ab_0
-  - markdown-it-py=3.0.0=pyhd8ed1ab_0
-  - matplotlib-base=3.7.2=py310hf38f957_0
-  - mdurl=0.1.0=pyhd8ed1ab_0
-  - multiqc=1.15=pyhdfd78af_0
-  - munkres=1.1.4=pyh9f0ad1d_0
-  - ncbi-vdb=3.0.0=pl5321h87f3376_0
-  - ncurses=6.4=hcb278e6_0
-  - networkx=3.1=pyhd8ed1ab_0
-  - oniguruma=6.9.8=h166bdaf_0
-  - openjdk=20.0.2=hfea2f88_1
-  - openjpeg=2.5.0=hfec8fc6_2
-  - openssl=3.3.0=hd590300_0
-  - packaging=23.1=pyhd8ed1ab_0
-  - pango=1.50.14=ha41ecd1_2
-  - pbzip2=1.1.13=0
-  - pcre=8.45=h9c3ff4c_0
-  - pcre2=10.40=hc3806b6_0
-  - perl=5.32.1=4_hd590300_perl5
-  - perl-archive-tar=2.40=pl5321hdfd78af_0
-  - perl-carp=1.50=pl5321hd8ed1ab_0
-  - perl-common-sense=3.75=pl5321hd8ed1ab_0
-  - perl-compress-raw-bzip2=2.201=pl5321h166bdaf_0
-  - perl-compress-raw-zlib=2.202=pl5321h166bdaf_0
-  - perl-encode=3.19=pl5321h166bdaf_0
-  - perl-exporter=5.74=pl5321hd8ed1ab_0
-  - perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0
-  - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
-  - perl-io-compress=2.201=pl5321hdbdd923_2
-  - perl-io-zlib=1.14=pl5321hdfd78af_0
-  - perl-json=4.10=pl5321hdfd78af_0
-  - perl-json-xs=2.34=pl5321h4ac6f70_6
-  - perl-list-moreutils=0.430=pl5321hdfd78af_0
-  - perl-list-moreutils-xs=0.430=pl5321h031d066_2
-  - perl-parent=0.241=pl5321hd8ed1ab_0
-  - perl-pathtools=3.75=pl5321h166bdaf_0
-  - perl-scalar-list-utils=1.63=pl5321h166bdaf_0
-  - perl-storable=3.15=pl5321h166bdaf_0
-  - perl-types-serialiser=1.01=pl5321hdfd78af_0
-  - pigz=2.6=h27826a3_0
-  - pip=23.2.1=pyhd8ed1ab_0
-  - pixman=0.40.0=h36c2ea0_0
-  - pthread-stubs=0.4=h36c2ea0_1001
-  - pycparser=2.21=pyhd8ed1ab_0
-  - pygments=2.16.1=pyhd8ed1ab_0
-  - pyparsing=3.0.9=pyhd8ed1ab_0
-  - pysocks=1.7.1=pyha2e5f31_6
-  - python=3.10.12=hd12c33a_0_cpython
-  - python-dateutil=2.8.2=pyhd8ed1ab_0
-  - python-isal=1.2.0=py310h2372a71_0
-  - python-tzdata=2023.3=pyhd8ed1ab_0
-  - python_abi=3.10=3_cp310
-  - pytz=2023.3.post1=pyhd8ed1ab_0
-  - qualimap=2.2.2d=hdfd78af_2
-  - r-base=4.2.3=hbfee4d0_7
-  - r-bh=1.81.0_1=r42hc72bb7e_1
-  - r-bitops=1.0_7=r42h57805ef_2
-  - r-codetools=0.2_19=r42hc72bb7e_1
-  - r-cpp11=0.4.6=r42hc72bb7e_0
-  - r-crayon=1.5.2=r42hc72bb7e_2
-  - r-formatr=1.14=r42hc72bb7e_1
-  - r-futile.logger=1.4.3=r42hc72bb7e_1005
-  - r-futile.options=1.0.1=r42hc72bb7e_1004
-  - r-getopt=1.20.3=r42ha770c72_4
-  - r-lambda.r=1.2.4=r42hc72bb7e_3
-  - r-lattice=0.21_8=r42h57805ef_1
-  - r-matrix=1.6_1=r42h316c678_0
-  - r-matrixstats=1.0.0=r42h57805ef_1
-  - r-optparse=1.7.3=r42hc72bb7e_2
-  - r-rcurl=1.98_1.12=r42hf9611b0_3
-  - r-restfulr=0.0.15=r42h56115f1_2
-  - r-rjson=0.2.21=r42ha503ecb_3
-  - r-snow=0.4_4=r42hc72bb7e_2
-  - r-xml=3.99_0.14=r42hc38eee6_2
-  - r-yaml=2.3.7=r42h57805ef_1
-  - readline=8.2=h8228510_1
-  - requests=2.31.0=pyhd8ed1ab_0
-  - rich=13.5.1=pyhd8ed1ab_0
-  - rich-click=1.6.1=pyhd8ed1ab_0
-  - samtools=1.17=hd87286a_1
-  - sed=4.8=he412f7d_0
-  - setuptools=68.1.2=pyhd8ed1ab_0
-  - six=1.16.0=pyh6c4a22f_0
-  - spectra=0.0.11=py_1
-  - sysroot_linux-64=2.12=he073ed8_16
-  - tk=8.6.12=h27826a3_0
-  - tktable=2.10=hb7b940f_3
-  - toml=0.10.2=pyhd8ed1ab_0
-  - tomlkit=0.12.1=pyha770c72_0
-  - typing_extensions=4.7.1=pyha770c72_0
-  - tzdata=2023c=h71feb2d_0
-  - urllib3=2.0.4=pyhd8ed1ab_0
-  - wget=1.20.3=ha35d2d1_1
-  - wheel=0.41.2=pyhd8ed1ab_0
-  - xmltodict=0.13.0=pyhd8ed1ab_0
-  - xorg-fixesproto=5.0=h7f98852_1002
-  - xorg-inputproto=2.3.2=h7f98852_1002
-  - xorg-kbproto=1.0.7=h7f98852_1002
-  - xorg-libice=1.1.1=hd590300_0
-  - xorg-libsm=1.2.4=h7391055_0
-  - xorg-libx11=1.8.6=h8ee46fc_0
-  - xorg-libxau=1.0.11=hd590300_0
-  - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xorg-libxext=1.3.4=h0b41bf4_2
-  - xorg-libxfixes=5.0.3=h7f98852_1004
-  - xorg-libxi=1.7.10=h7f98852_0
-  - xorg-libxrender=0.9.11=hd590300_0
-  - xorg-libxt=1.3.0=hd590300_1
-  - xorg-libxtst=1.2.3=h7f98852_1002
-  - xorg-recordproto=1.14.2=h7f98852_1002
-  - xorg-renderproto=0.11.1=h7f98852_1002
-  - xorg-xextproto=7.3.0=h0b41bf4_1003
-  - xorg-xproto=7.0.31=h7f98852_1007
-  - xz=5.2.6=h166bdaf_0
-  - yaml=0.2.5=h7f98852_2
-  - yq=3.2.3=pyhd8ed1ab_0
-  - zipp=3.16.2=pyhd8ed1ab_0
-  - zlib=1.2.13=hd590300_5
-  - zstd=1.5.2=hfc55251_7
-  - pip:
-    - biopython==1.81
-    - brotli==1.1.0
-    - cffi==1.15.1
-    - contourpy==1.1.0
-    - cutadapt==4.4
-    - dnaio==1.0.0
-    - fonttools==4.42.1
-    - humanfriendly==10.0
-    - isal==1.2.0
-    - kiwisolver==1.4.5
-    - markupsafe==2.1.3
-    - matplotlib==3.7.2
-    - numpy==1.25.2
-    - openpyxl==3.1.2
-    - pandas==2.1.0
-    - pillow==10.0.0
-    - pyyaml==6.0.1
-    - simplejson==3.19.1
-    - unicodedata2==15.0.0
-    - xopen==1.7.0
-    - zstandard==0.19.0
+  - fastp=0.23.2
+  - cutadapt=4.4
+  - multiqc=1.15
+  - fastqc=0.12.1
+  - genoflu=1.03