Merge pull request #54 from RickGelhausen/1.7.0

Updated to version 1.7.0
RickGelhausen · May 9, 2023 · 0d51690 · 0d51690
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,3 +1,12 @@
+### version 1.7.0 [Rick Gelhausen](mailto:gelhausr@informatik.uni-freiburg.de) 24.02.2023
+ * improved Snakefile and added validation for config file
+ * updated config file structure
+ * added 3D PCA plots for quality control
+ * added 2D PCA plots + hierarchical clustering of read counts for quality control
+ * fixed error that caused crashes when annotation had extra plasmids not present in genome file
+ * updated manual
+ * updated ReadTheDocs
+
 ### version 1.6.2 [Rick Gelhausen](mailto:gelhausr@informatik.uni-freiburg.de) 04.10.2022
  * fixed bug where the new input tables were not correctly created depending on the input contrast.
  * fixed bug with wrong condition vector labeling causing incorrect behavior in riborex log2FC calculation

diff --git a/Snakefile b/Snakefile
diff --git a/environment.yaml b/environment.yaml
@@ -0,0 +1,188 @@
+name: hribo_env
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - aioeasywebdav=2.4.0=pyha770c72_0
+  - aiohttp=3.8.4=py311h2582759_0
+  - aiosignal=1.3.1=pyhd8ed1ab_0
+  - amply=0.1.5=pyhd8ed1ab_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - async-timeout=4.0.2=pyhd8ed1ab_0
+  - attmap=0.13.2=pyhd8ed1ab_0
+  - attrs=22.2.0=pyh71513ae_0
+  - backports=1.0=pyhd8ed1ab_3
+  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
+  - bcrypt=3.2.2=py311hd4cff14_1
+  - boto3=1.26.92=pyhd8ed1ab_0
+  - botocore=1.29.93=pyhd8ed1ab_0
+  - brotlipy=0.7.0=py311hd4cff14_1005
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.18.1=h7f98852_0
+  - ca-certificates=2022.12.7=ha878542_0
+  - cachetools=5.3.0=pyhd8ed1ab_0
+  - certifi=2022.12.7=pyhd8ed1ab_0
+  - cffi=1.15.1=py311h409f033_3
+  - charset-normalizer=2.1.1=pyhd8ed1ab_0
+  - cni=1.0.1=ha975731_1
+  - cni-plugins=1.0.1=ha8f183a_0
+  - coin-or-cbc=2.10.8=h3786ebc_0
+  - coin-or-cgl=0.60.6=h6f57e76_2
+  - coin-or-clp=1.17.7=hc56784d_2
+  - coin-or-osi=0.108.7=h2720bb7_2
+  - coin-or-utils=2.11.6=h202d8b1_2
+  - coincbc=2.10.8=0_metapackage
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - configargparse=1.5.3=pyhd8ed1ab_0
+  - connection_pool=0.0.3=pyhd3deb0d_0
+  - cryptography=39.0.2=py311h9b4c7bb_0
+  - datrie=0.8.2=py311hd4cff14_6
+  - defusedxml=0.7.1=pyhd8ed1ab_0
+  - docutils=0.19=py311h38be061_1
+  - dpath=2.1.4=py311h38be061_0
+  - dropbox=11.36.0=pyhd8ed1ab_0
+  - exceptiongroup=1.1.1=pyhd8ed1ab_0
+  - filechunkio=1.8=py_2
+  - filelock=3.10.0=pyhd8ed1ab_0
+  - frozenlist=1.3.3=py311hd4cff14_0
+  - ftputil=5.0.4=pyhd8ed1ab_0
+  - gitdb=4.0.10=pyhd8ed1ab_0
+  - gitpython=3.1.31=pyhd8ed1ab_0
+  - google-api-core=2.11.0=pyhd8ed1ab_0
+  - google-api-python-client=2.81.0=pyhd8ed1ab_0
+  - google-auth=2.16.2=pyh1a96a4e_0
+  - google-auth-httplib2=0.1.0=pyhd8ed1ab_1
+  - google-cloud-core=2.3.2=pyhd8ed1ab_0
+  - google-cloud-storage=2.7.0=pyh1a96a4e_0
+  - google-crc32c=1.1.2=py311h98db957_4
+  - google-resumable-media=2.4.1=pyhd8ed1ab_0
+  - googleapis-common-protos=1.57.1=pyhd8ed1ab_0
+  - grpcio=1.52.1=py311hcafe171_1
+  - httplib2=0.21.0=pyhd8ed1ab_0
+  - humanfriendly=10.0=py311h38be061_4
+  - icu=70.1=h27087fc_0
+  - idna=3.4=pyhd8ed1ab_0
+  - importlib-metadata=6.0.0=pyha770c72_0
+  - importlib_resources=5.12.0=pyhd8ed1ab_0
+  - iniconfig=2.0.0=pyhd8ed1ab_0
+  - jinja2=3.1.2=pyhd8ed1ab_1
+  - jmespath=1.0.1=pyhd8ed1ab_0
+  - jq=1.6=h36c2ea0_1000
+  - jsonschema=4.17.3=pyhd8ed1ab_0
+  - jupyter_core=5.3.0=py311h38be061_0
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - libabseil=20230125.0=cxx17_hcb278e6_1
+  - libarchive=3.5.2=hada088e_3
+  - libblas=3.9.0=16_linux64_openblas
+  - libcblas=3.9.0=16_linux64_openblas
+  - libcrc32c=1.1.2=h9c3ff4c_0
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=12.2.0=h65d4601_19
+  - libgfortran-ng=12.2.0=h69a702a_19
+  - libgfortran5=12.2.0=h337968e_19
+  - libgomp=12.2.0=h65d4601_19
+  - libgrpc=1.52.1=hcf146ea_1
+  - libiconv=1.17=h166bdaf_0
+  - liblapack=3.9.0=16_linux64_openblas
+  - liblapacke=3.9.0=16_linux64_openblas
+  - libnsl=2.0.0=h7f98852_0
+  - libopenblas=0.3.21=pthreads_h78a6416_3
+  - libprotobuf=3.21.12=h3eb15da_0
+  - libseccomp=2.4.4=h166bdaf_3
+  - libsodium=1.0.18=h36c2ea0_1
+  - libsqlite=3.40.0=h753d276_0
+  - libstdcxx-ng=12.2.0=h46fd767_19
+  - libuuid=2.32.1=h7f98852_1000
+  - libxml2=2.10.3=hca2bb57_3
+  - libzlib=1.2.13=h166bdaf_4
+  - logmuse=0.2.6=pyh8c360ce_0
+  - lz4-c=1.9.4=hcb278e6_0
+  - lzo=2.10=h516909a_1000
+  - markdown-it-py=2.2.0=pyhd8ed1ab_0
+  - markupsafe=2.1.2=py311h2582759_0
+  - mdurl=0.1.0=pyhd8ed1ab_0
+  - multidict=6.0.4=py311h2582759_0
+  - nbformat=5.7.3=pyhd8ed1ab_0
+  - ncurses=6.3=h27087fc_1
+  - numpy=1.24.2=py311h8e6699e_0
+  - oauth2client=4.1.3=py_0
+  - oniguruma=6.9.8=h166bdaf_0
+  - openssl=3.1.0=h0b41bf4_0
+  - packaging=23.0=pyhd8ed1ab_0
+  - pandas=1.5.3=py311h2872171_0
+  - paramiko=3.1.0=pyhd8ed1ab_0
+  - peppy=0.35.4=pyhd8ed1ab_0
+  - pip=23.0.1=pyhd8ed1ab_0
+  - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
+  - plac=1.3.5=pyhd8ed1ab_0
+  - platformdirs=3.1.1=pyhd8ed1ab_0
+  - pluggy=1.0.0=pyhd8ed1ab_5
+  - ply=3.11=py_1
+  - prettytable=3.6.0=pyhd8ed1ab_0
+  - protobuf=4.21.12=py311hcafe171_0
+  - psutil=5.9.4=py311hd4cff14_0
+  - pulp=2.7.0=py311h38be061_0
+  - pyasn1=0.4.8=py_0
+  - pyasn1-modules=0.2.7=py_0
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pygments=2.14.0=pyhd8ed1ab_0
+  - pynacl=1.5.0=py311hd4cff14_2
+  - pyopenssl=23.0.0=pyhd8ed1ab_0
+  - pyparsing=3.0.9=pyhd8ed1ab_0
+  - pyrsistent=0.19.3=py311h2582759_0
+  - pysftp=0.2.9=py_1
+  - pysocks=1.7.1=pyha2e5f31_6
+  - pytest=7.2.2=pyhd8ed1ab_0
+  - python=3.11.0=he550d4f_1_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-fastjsonschema=2.16.3=pyhd8ed1ab_0
+  - python-irodsclient=1.1.6=pyhd8ed1ab_0
+  - python_abi=3.11=3_cp311
+  - pytz=2022.7.1=pyhd8ed1ab_0
+  - pyu2f=0.1.5=pyhd8ed1ab_0
+  - pyyaml=6.0=py311hd4cff14_5
+  - re2=2023.02.02=hcb278e6_0
+  - readline=8.1.2=h0f457ee_0
+  - requests=2.28.2=pyhd8ed1ab_0
+  - reretry=0.11.8=pyhd8ed1ab_0
+  - rich=13.3.2=pyhd8ed1ab_0
+  - rsa=4.9=pyhd8ed1ab_0
+  - s3transfer=0.6.0=pyhd8ed1ab_0
+  - setuptools=67.6.0=pyhd8ed1ab_0
+  - setuptools-scm=7.1.0=pyhd8ed1ab_0
+  - singularity=3.8.6=hf1ae047_0
+  - six=1.16.0=pyh6c4a22f_0
+  - slacker=0.14.0=py_0
+  - smart_open=6.3.0=pyhd8ed1ab_1
+  - smmap=3.0.5=pyh44b312d_0
+  - snakemake=7.24.2=hdfd78af_0
+  - snakemake-minimal=7.24.2=pyhdfd78af_0
+  - squashfs-tools=4.4=hd0129a2_3
+  - stone=3.3.1=pyhd8ed1ab_0
+  - stopit=1.1.2=py_0
+  - tabulate=0.9.0=pyhd8ed1ab_1
+  - throttler=1.2.1=pyhd8ed1ab_0
+  - tk=8.6.12=h27826a3_0
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - toposort=1.10=pyhd8ed1ab_0
+  - traitlets=5.9.0=pyhd8ed1ab_0
+  - typing-extensions=4.5.0=hd8ed1ab_0
+  - typing_extensions=4.5.0=pyha770c72_0
+  - tzdata=2022g=h191b570_0
+  - ubiquerg=0.6.2=pyhd8ed1ab_0
+  - uritemplate=4.1.1=pyhd8ed1ab_0
+  - urllib3=1.26.15=pyhd8ed1ab_0
+  - veracitools=0.1.3=py_0
+  - wcwidth=0.2.6=pyhd8ed1ab_0
+  - wheel=0.40.0=pyhd8ed1ab_0
+  - wrapt=1.15.0=py311h2582759_0
+  - xz=5.2.6=h166bdaf_0
+  - yaml=0.2.5=h7f98852_2
+  - yarl=1.8.2=py311hd4cff14_0
+  - yte=1.5.1=py311h38be061_1
+  - zipp=3.15.0=pyhd8ed1ab_0
+  - zlib=1.2.13=h166bdaf_4
+  - zstd=1.5.2=h3eb15da_6
diff --git a/envs/deseq2.yaml b/envs/deseq2.yaml
@@ -0,0 +1,8 @@
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - r-optparse =1.7.3
+ - r-plyr =1.8.8
+ - bioconductor-deseq2 =1.38.0
+ - r-ggplot2 =3.4.0
diff --git a/envs/metageneprofiling.yaml b/envs/metageneprofiling.yaml
@@ -4,9 +4,9 @@ channels:
 dependencies:
  - numpy
  - pysam
- - regex
- - matplotlib
  - pandas
  - interlap
+ - plotly
+ - xlsxwriter
  - openpyxl
- - scipy
+ - python-kaleido
diff --git a/envs/plotly.yaml b/envs/plotly.yaml
@@ -0,0 +1,6 @@
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - pandas =1.5.2
+ - plotly =5.11.0
diff --git a/envs/pytools.yaml b/envs/pytools.yaml
@@ -2,5 +2,5 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - pandas =0.24.2
- - pysam =0.15.2
+ - pandas =1.5.2
+ - pysam =0.19.1
diff --git a/envs/reparation.yaml b/envs/reparation.yaml
@@ -2,4 +2,5 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - reparation_blast=1.0.9=pl526_1
+ - python=3.7.12
+ - reparation_blast=1.0.9
diff --git a/envs/subread.yaml b/envs/subread.yaml
@@ -2,5 +2,5 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - subread =1.6.3
- - pandas =0.24.2
+ - subread =2.0.1
+ - pandas =1.5.2
diff --git a/envs/xtail.yaml b/envs/xtail.yaml
@@ -6,4 +6,4 @@ dependencies:
  - xtail =1.1.5
  - r-optparse =1.6.0
  - r-plyr =1.8.6
- - libgfortran-ng =7.2.0
+ - libgfortran-ng
diff --git a/manual/Manual_HRIBO.pdf b/manual/Manual_HRIBO.pdf
diff --git a/report/annotation.rst b/report/annotation.rst
diff --git a/report/centeredwig.rst b/report/centeredwig.rst
diff --git a/report/combined.rst b/report/combined.rst
diff --git a/report/combined_annotation.rst b/report/combined_annotation.rst
diff --git a/report/correlation.rst b/report/correlation.rst
diff --git a/report/fastqcmapped.rst b/report/fastqcmapped.rst
diff --git a/report/fastqcnorRNA.rst b/report/fastqcnorRNA.rst
diff --git a/report/fastqcraw.rst b/report/fastqcraw.rst
diff --git a/report/fastqctrimmed.rst b/report/fastqctrimmed.rst
diff --git a/report/fiveprimewig.rst b/report/fiveprimewig.rst
diff --git a/report/genome.rst b/report/genome.rst
diff --git a/report/globalwig.rst b/report/globalwig.rst
diff --git a/report/multiqc.rst b/report/multiqc.rst
diff --git a/report/novelall.rst b/report/novelall.rst
diff --git a/report/novelannotation.rst b/report/novelannotation.rst
diff --git a/report/novelfiltered.rst b/report/novelfiltered.rst
diff --git a/report/novelmerged.rst b/report/novelmerged.rst
diff --git a/report/rbsTrack.rst b/report/rbsTrack.rst
diff --git a/report/reparation_metagene.rst b/report/reparation_metagene.rst
diff --git a/report/reparation_psite.rst b/report/reparation_psite.rst
diff --git a/report/reparation_roc.rst b/report/reparation_roc.rst
diff --git a/report/reparation_scurve.rst b/report/reparation_scurve.rst
diff --git a/report/riborex.rst b/report/riborex.rst
diff --git a/report/ribotish.rst b/report/ribotish.rst
diff --git a/report/ribotishquality.rst b/report/ribotishquality.rst
diff --git a/report/startCodons.rst b/report/startCodons.rst
diff --git a/report/stopCodons.rst b/report/stopCodons.rst
diff --git a/report/summary.rst b/report/summary.rst
diff --git a/report/summaryxlsx.rst b/report/summaryxlsx.rst
diff --git a/report/threeprimewig.rst b/report/threeprimewig.rst
diff --git a/report/wig.rst b/report/wig.rst
diff --git a/report/workflow.rst b/report/workflow.rst
diff --git a/report/workflow_nixtail.rst b/report/workflow_nixtail.rst
diff --git a/report/xtail_fc.rst b/report/xtail_fc.rst
diff --git a/report/xtail_r.rst b/report/xtail_r.rst
diff --git a/report/xtail_table.rst b/report/xtail_table.rst