diff --git a/nextflow/nf_rna.yaml b/nextflow/nf_rna.yaml new file mode 100644 index 0000000..9fb25ea --- /dev/null +++ b/nextflow/nf_rna.yaml @@ -0,0 +1,333 @@ +name: nf_rna +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - _r-mutex=1.0.1=anacondar_1 + - alsa-lib=1.2.11=hd590300_1 + - annotated-types=0.7.0=pyhd8ed1ab_0 + - binutils_impl_linux-64=2.40=ha1999f0_7 + - biopet-validatefastq=0.1.1=hdfd78af_3 + - brotli-python=1.1.0=py311hb755f60_1 + - bwidget=1.9.14=ha770c72_1 + - bx-python=0.11.0=py311h312114e_2 + - bzip2=1.0.8=hd590300_5 + - c-ares=1.28.1=hd590300_0 + - ca-certificates=2024.7.4=hbcca054_0 + - cairo=1.18.0=h3faef2a_0 + - certifi=2024.7.4=pyhd8ed1ab_0 + - charset-normalizer=3.3.2=pyhd8ed1ab_0 + - click=8.1.7=unix_pyh707e725_0 + - colorama=0.4.6=pyhd8ed1ab_0 + - coloredlogs=15.0.1=pyhd8ed1ab_3 + - colormath=3.0.0=py_2 + - curl=8.8.0=he654da7_0 + - entrez-direct=22.1=he881be0_0 + - expat=2.6.2=h59595ed_0 + - fastp=0.23.4=h125f33a_4 + - 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=h77eed37_2 + - fontconfig=2.14.2=h14ed4e7_0 + - fonts-conda-ecosystem=1=0 + - fonts-conda-forge=1=0 + - freetype=2.12.1=h267a509_2 + - fribidi=1.0.10=h36c2ea0_0 + - gcc_impl_linux-64=13.2.0=h9eb54c0_13 + - gettext=0.22.5=h59595ed_2 + - gettext-tools=0.22.5=h59595ed_2 + - gfortran_impl_linux-64=13.2.0=h9efe08d_13 + - giflib=5.2.2=hd590300_0 + - graphite2=1.3.13=h59595ed_1003 + - gxx_impl_linux-64=13.2.0=h2a599c4_13 + - harfbuzz=8.5.0=hfac3d4d_0 + - htslib=1.20=h5efdd21_1 + - humanfriendly=10.0=pyhd8ed1ab_6 + - humanize=4.9.0=pyhd8ed1ab_0 + - icu=73.2=h59595ed_0 + - idna=3.7=pyhd8ed1ab_0 + - importlib-metadata=7.2.1=pyha770c72_0 + - importlib_metadata=7.2.1=hd8ed1ab_0 + - isa-l=2.31.0=hd590300_1 + - jinja2=3.1.4=pyhd8ed1ab_0 + - kaleido-core=0.2.1=h3644ca4_0 + - kernel-headers_linux-64=2.6.32=he073ed8_17 + - keyutils=1.6.1=h166bdaf_0 + - krb5=1.21.2=h659d440_0 + - lcms2=2.16=hb7c19ff_0 + - ld_impl_linux-64=2.40=hf3520f5_7 + - lerc=4.0.0=h27087fc_0 + - libasprintf=0.22.5=h661eb56_2 + - libasprintf-devel=0.22.5=h661eb56_2 + - libblas=3.9.0=22_linux64_openblas + - libcblas=3.9.0=22_linux64_openblas + - libcups=2.3.3=h4637d8d_4 + - libcurl=8.8.0=hca28451_0 + - libdeflate=1.20=hd590300_0 + - libedit=3.1.20191231=he28a2e2_2 + - libev=4.33=hd590300_2 + - libexpat=2.6.2=h59595ed_0 + - libffi=3.4.2=h7f98852_5 + - libgcc-devel_linux-64=13.2.0=hdb50d1a_113 + - libgcc-ng=13.2.0=h77fa898_12 + - libgettextpo=0.22.5=h59595ed_2 + - libgettextpo-devel=0.22.5=h59595ed_2 + - libgfortran-ng=13.2.0=h69a702a_13 + - libgfortran5=13.2.0=h3d2ce59_13 + - libglib=2.80.2=hf974151_0 + - libgomp=13.2.0=h77fa898_12 + - libiconv=1.17=hd590300_2 + - libidn2=2.3.7=hd590300_0 + - libjpeg-turbo=3.0.0=hd590300_1 + - liblapack=3.9.0=22_linux64_openblas + - libnghttp2=1.58.0=h47da74e_1 + - libnsl=2.0.1=hd590300_0 + - libopenblas=0.3.27=pthreads_h413a1c8_0 + - libpng=1.6.43=h2797004_0 + - libsanitizer=13.2.0=h6ddb7a1_13 + - libsqlite=3.46.0=hde9e2c9_0 + - libssh2=1.11.0=h0841786_0 + - libstdcxx-devel_linux-64=13.2.0=hdb50d1a_113 + - libstdcxx-ng=13.2.0=hc0a3c3a_12 + - libtiff=4.6.0=h1dd3fc0_3 + - libunistring=0.9.10=h7f98852_0 + - libuuid=2.38.1=h0b41bf4_0 + - libwebp-base=1.4.0=hd590300_0 + - libxcb=1.15=h0b41bf4_0 + - libxcrypt=4.4.36=hd590300_1 + - libzlib=1.2.13=h4ab18f5_6 + - make=4.3=hd18ef5c_1 + - markdown=3.6=pyhd8ed1ab_0 + - markdown-it-py=3.0.0=pyhd8ed1ab_0 + - markupsafe=2.1.5=py311h459d7ec_0 + - mathjax=2.7.7=ha770c72_3 + - mdurl=0.1.2=pyhd8ed1ab_0 + - multiqc=1.22.3=pyhdfd78af_0 + - ncurses=6.5=h59595ed_0 + - networkx=3.3=pyhd8ed1ab_1 + - nspr=4.35=h27087fc_0 + - nss=3.100=hca3bf56_0 + - numpy=1.26.4=py311h64a7726_0 + - openjdk=8.0.412=hd590300_1 + - openjpeg=2.5.2=h488ebb8_0 + - openssl=3.3.1=h4bc722e_2 + - packaging=24.1=pyhd8ed1ab_0 + - pandas=2.2.2=py311h14de704_1 + - pango=1.54.0=h84a9a3c_0 + - pcre2=10.43=hcad00b1_0 + - perl=5.32.1=7_hd590300_perl5 + - pillow=10.3.0=py311h18e6fac_0 + - pip=24.0=pyhd8ed1ab_0 + - pixman=0.43.2=h59595ed_0 + - plotly=5.22.0=pyhd8ed1ab_0 + - pthread-stubs=0.4=h36c2ea0_1001 + - pyaml-env=1.1.0=pyhd8ed1ab_0 + - pybigwig=0.3.22=py311hc40ab17_3 + - pydantic=2.7.4=pyhd8ed1ab_0 + - pydantic-core=2.18.4=py311h5ecf98a_0 + - pygments=2.18.0=pyhd8ed1ab_0 + - pysam=0.22.1=py311h1f0e11c_1 + - pysocks=1.7.1=pyha2e5f31_6 + - python=3.11.9=hb806964_0_cpython + - python-dateutil=2.9.0=pyhd8ed1ab_0 + - python-kaleido=0.2.1=pyhd8ed1ab_0 + - python-tzdata=2024.1=pyhd8ed1ab_0 + - python_abi=3.11=4_cp311 + - pytz=2024.1=pyhd8ed1ab_0 + - pyyaml=5.4.1=py311hd4cff14_4 + - r-base=4.4.0=h019f4a6_1 + - readline=8.2=h8228510_1 + - requests=2.32.3=pyhd8ed1ab_0 + - rich=13.7.1=pyhd8ed1ab_0 + - rich-click=1.8.3=pyhd8ed1ab_0 + - rseqc=5.0.3=py311hdad781d_2 + - samtools=1.20=h50ea8bc_0 + - sed=4.8=he412f7d_0 + - setuptools=70.1.1=pyhd8ed1ab_0 + - six=1.16.0=pyh6c4a22f_0 + - spectra=0.0.11=py_1 + - sqlite=3.46.0=h6d4b2fc_0 + - sra-tools=2.9.6=hf484d3e_0 + - star=2.7.11b=h43eeafb_1 + - subread=2.0.6=he4a0461_2 + - sysroot_linux-64=2.12=he073ed8_17 + - tenacity=8.4.2=pyhd8ed1ab_0 + - tk=8.6.13=noxft_h4845f30_101 + - tktable=2.10=h8bc8fbc_6 + - tqdm=4.66.4=pyhd8ed1ab_0 + - typeguard=4.3.0=pyhd8ed1ab_0 + - typing-extensions=4.12.2=hd8ed1ab_0 + - typing_extensions=4.12.2=pyha770c72_0 + - tzdata=2024a=h0c530f3_0 + - urllib3=2.2.2=pyhd8ed1ab_0 + - wget=1.21.4=hda4d442_0 + - wheel=0.43.0=pyhd8ed1ab_1 + - 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=1.8.9=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 + - zipp=3.19.2=pyhd8ed1ab_0 + - zlib=1.2.13=h4ab18f5_6 + - zstd=1.5.6=ha6fb4c9_0 + - pip: + - accessible-pygments==0.0.5 + - alabaster==1.0.0 + - anyio==4.4.0 + - appdirs==1.4.4 + - argon2-cffi==23.1.0 + - argon2-cffi-bindings==21.2.0 + - arrow==1.3.0 + - asttokens==2.4.1 + - async-lru==2.0.4 + - attrs==23.2.0 + - babel==2.16.0 + - backports-tarfile==1.2.0 + - beautifulsoup4==4.12.3 + - bleach==6.1.0 + - cattrs==23.2.3 + - cffi==1.17.0 + - cfgv==3.4.0 + - comm==0.2.2 + - coverage==7.6.1 + - cryptography==43.0.0 + - debugpy==1.8.5 + - decorator==5.1.1 + - defusedxml==0.7.1 + - distlib==0.3.8 + - docutils==0.21.2 + - executing==2.0.1 + - fastjsonschema==2.20.0 + - filelock==3.15.4 + - fqdn==1.5.1 + - greenlet==3.0.3 + - h11==0.14.0 + - httpcore==1.0.5 + - httpx==0.27.0 + - identify==2.6.0 + - imagesize==1.4.1 + - iniconfig==2.0.0 + - ipykernel==6.29.5 + - ipython==8.26.0 + - isoduration==20.11.0 + - jaraco-classes==3.4.0 + - jaraco-context==5.3.0 + - jaraco-functools==4.0.2 + - jedi==0.19.1 + - jeepney==0.8.0 + - json5==0.9.25 + - jsonpointer==3.0.0 + - jsonschema==4.23.0 + - jsonschema-specifications==2023.12.1 + - jupyter-cache==1.0.0 + - jupyter-client==8.6.2 + - jupyter-core==5.7.2 + - jupyter-events==0.10.0 + - jupyter-lsp==2.2.5 + - jupyter-server==2.14.2 + - jupyter-server-terminals==0.5.3 + - jupyterlab==4.2.4 + - jupyterlab-pygments==0.3.0 + - jupyterlab-server==2.27.3 + - keyring==25.3.0 + - latexcodec==3.0.0 + - matplotlib-inline==0.1.7 + - mdit-py-plugins==0.4.1 + - mistune==3.0.2 + - more-itertools==10.4.0 + - myst-nb==1.1.1 + - myst-parser==4.0.0 + - nbclient==0.10.0 + - nbconvert==7.16.4 + - nbformat==5.10.4 + - nest-asyncio==1.6.0 + - nextflow==24.4.3 + - nf-rnaseq==0.0.1 + - nh3==0.2.18 + - nodeenv==1.9.1 + - notebook==7.2.1 + - notebook-shim==0.2.4 + - overrides==7.7.0 + - pandocfilters==1.5.1 + - parso==0.8.4 + - pexpect==4.9.0 + - pkginfo==1.10.0 + - platformdirs==4.2.2 + - pluggy==1.5.0 + - pre-commit==3.8.0 + - prometheus-client==0.20.0 + - prompt-toolkit==3.0.47 + - psutil==6.0.0 + - ptyprocess==0.7.0 + - pure-eval==0.2.3 + - pybtex==0.24.0 + - pybtex-docutils==1.0.3 + - pycparser==2.22 + - pydata-sphinx-theme==0.15.4 + - pytest==8.3.2 + - python-json-logger==2.0.7 + - pyzmq==26.1.0 + - readme-renderer==44.0 + - referencing==0.35.1 + - requests-cache==0.9.8 + - requests-toolbelt==1.0.0 + - rfc3339-validator==0.1.4 + - rfc3986==2.0.0 + - rfc3986-validator==0.1.1 + - rpds-py==0.20.0 + - secretstorage==3.3.3 + - send2trash==1.8.3 + - session-info==1.0.0 + - sniffio==1.3.1 + - snowballstemmer==2.2.0 + - soupsieve==2.5 + - sphinx==8.0.2 + - sphinx-autodoc-typehints==2.2.3 + - sphinx-book-theme==1.1.3 + - sphinx-copybutton==0.5.2 + - sphinxcontrib-applehelp==2.0.0 + - sphinxcontrib-bibtex==2.6.2 + - sphinxcontrib-devhelp==2.0.0 + - sphinxcontrib-htmlhelp==2.1.0 + - sphinxcontrib-jsmath==1.0.1 + - sphinxcontrib-qthelp==2.0.0 + - sphinxcontrib-serializinghtml==2.0.0 + - sphinxext-opengraph==0.9.1 + - sqlalchemy==2.0.32 + - stack-data==0.6.3 + - stdlib-list==0.10.0 + - tabulate==0.9.0 + - terminado==0.18.1 + - tinycss2==1.3.0 + - tornado==6.4.1 + - traitlets==5.14.3 + - twine==5.1.1 + - types-python-dateutil==2.9.0.20240316 + - uri-template==1.3.0 + - url-normalize==1.4.3 + - virtualenv==20.26.3 + - wcwidth==0.2.13 + - webcolors==24.8.0 + - webencodings==0.5.1 + - websocket-client==1.8.0 +prefix: /home/whitej6/miniforge3/envs/nf_rna