Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Dev #370

Merged
merged 20 commits into from
Jul 16, 2024
Merged

Dev #370

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
20 commits
Select commit Hold shift + click to select a range
e3b6c64
add drugs to collate variants
jodyphelan May 13, 2024
2d2efaa
bump version
jodyphelan May 13, 2024
32d4c27
bug fix for spoligo
jodyphelan May 23, 2024
67ac8f8
add macos env
jodyphelan Jun 7, 2024
3428202
adding in depth to txt output
jodyphelan Jun 21, 2024
4c50d84
fix for #366
jodyphelan Jun 21, 2024
389ae5b
improve docx output
jodyphelan Jun 23, 2024
d048c1e
remove verbose
jodyphelan Jun 23, 2024
1be0fcd
add debug
jodyphelan Jun 23, 2024
9764fa6
update docx
jodyphelan Jun 23, 2024
e2620a5
update conda env
jodyphelan Jun 24, 2024
fc2d0fd
variant calling classes
jodyphelan Jul 4, 2024
889f2aa
style
jodyphelan Jul 4, 2024
bc23fd9
bug
jodyphelan Jul 4, 2024
e5893ad
add --debug
jodyphelan Jul 4, 2024
a9f39c1
text output bugfix
jodyphelan Jul 5, 2024
609801b
add version to schema
jodyphelan Jul 5, 2024
14e51ff
update schema version
jodyphelan Jul 5, 2024
bda746e
add variant calling classes
jodyphelan Jul 16, 2024
f66729f
update version
jodyphelan Jul 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 14 additions & 13 deletions conda/linux-latest.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,8 @@
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/bioconda/linux-64/seqkit-2.8.0-h9ee0642_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
Expand All @@ -13,6 +12,7 @@ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_4.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/linux-64/mpi-1.0-openmpi.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-4_cp310.conda
https://conda.anaconda.org/bioconda/linux-64/seqkit-2.8.2-h9ee0642_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/tzdata-2023d-h0c530f3_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_4.conda
Expand Down Expand Up @@ -49,7 +49,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.cond
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_2.conda
https://conda.anaconda.org/conda-forge/linux-64/oniguruma-6.9.9-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.1-h4ab18f5_0.conda
https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/linux-64/wfa2-lib-2.3.4-h4ac6f70_0.tar.bz2
Expand Down Expand Up @@ -115,7 +115,7 @@ https://conda.anaconda.org/conda-forge/noarch/bitstring-3.1.9-pyhd8ed1ab_0.tar.b
https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hd590300_1.conda
https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py310hc6cd4ac_1.conda
https://conda.anaconda.org/conda-forge/noarch/cachetools-4.2.4-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/certifi-2024.6.2-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda
Expand All @@ -138,10 +138,8 @@ https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.0-h488ebb8_3.conda
https://conda.anaconda.org/conda-forge/noarch/packaging-23.2-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/pygments-2.17.2-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/pyparsing-3.1.2-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/pyparsing-3.1.1-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha2e5f31_6.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2023.4-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/pytz-2023.4-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/setuptools-69.0.3-pyhd8ed1ab_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2
Expand All @@ -154,8 +152,9 @@ https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda
https://conda.anaconda.org/conda-forge/linux-64/cffi-1.16.0-py310h2fee648_0.conda
https://conda.anaconda.org/conda-forge/linux-64/curl-8.5.0-hca28451_0.conda
https://conda.anaconda.org/conda-forge/noarch/deprecation-2.1.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.49.0-py310h2372a71_0.conda
https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.47.2-py310h2372a71_0.conda
https://conda.anaconda.org/bioconda/linux-64/htslib-1.19.1-h81da01d_0.tar.bz2
https://conda.anaconda.org/bioconda/noarch/itol-config-0.1.0-pyhdfd78af_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.3-pyhd8ed1ab_0.conda
Expand All @@ -172,11 +171,12 @@ https://conda.anaconda.org/conda-forge/noarch/python-docx-1.1.0-pyhd8ed1ab_0.con
https://conda.anaconda.org/conda-forge/noarch/screed-1.1.3-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/tqdm-4.66.1-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.9.0-hd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/urllib3-2.1.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/linux-64/xorg-libxi-1.7.10-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.6.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/bioconda/linux-64/delly-1.2.6-hb7e2ac5_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/noarch/docxtpl-0.11.5-pyhd8ed1ab_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/git-2.43.0-pl5321h7bc287a_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.3.0-h3d44ed6_0.conda
https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.3-py310hb13e2d6_0.conda
Expand All @@ -191,17 +191,18 @@ https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.0-py310hd41b1e2_0.
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/linux-64/lofreq-2.1.5-py310h47ef89e_10.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/mash-2.3-ha9a2dd8_3.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/conda-forge/linux-64/openjdk-17.0.8-hbf40d96_2.conda
https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.0-py310hcc13569_0.conda
https://conda.anaconda.org/conda-forge/noarch/pydantic-2.6.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/rich-argparse-1.4.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/linux-64/scipy-1.12.0-py310hb13e2d6_2.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/linux-64/tabixpp-1.1.2-hd68fcf3_1.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/noarch/gatk4-4.4.0.0-py36hdfd78af_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.8.3-py310h62c0568_0.conda
https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.8.2-py310h62c0568_0.conda
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/noarch/pilon-1.24-hdfd78af_0.tar.bz2
https://conda.anaconda.org/bioconda/noarch/snpeff-5.2-hdfd78af_0.tar.bz2
https://conda.anaconda.org/t/no-15126f85-4dce-4462-b48d-9bc580ca6641/bioconda/noarch/trimmomatic-0.39-hdfd78af_2.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/vcflib-1.0.9-h146fbdb_4.tar.bz2
https://conda.anaconda.org/bioconda/linux-64/freebayes-1.3.6-hb0f3ef8_7.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/sourmash-minimal-4.8.6-py310h373cc83_0.conda
https://conda.anaconda.org/bioconda/noarch/sourmash-4.8.6-hdfd78af_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/sourmash-minimal-4.8.5-py310h373cc83_0.conda
https://conda.anaconda.org/bioconda/noarch/sourmash-4.8.5-hdfd78af_0.tar.bz2
https://conda.anaconda.org/bioconda/noarch/pathogen-profiler-4.2.0-pyh7cba7a3_0.tar.bz2
https://conda.anaconda.org/bioconda/noarch/tb-profiler-6.2.1-pyhdfd78af_0.tar.bz2
Loading
Loading