removing nextflow hidden files and folders

igsr_analysis.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: igsr-analysis
+Version: 1.0.1
+Summary: This package contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data.
+Home-page: https://github.com/igsr/igsr_analysis/archive/refs/tags/v1.0.1.tar.gz
+Author: Ernesto Lowy
+Author-email: [email protected]
+License: MIT
+Description: 
+        This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data 
+
+        The International Genome Sample Resource [(IGSR)](http://www.internationalgenome.org/) is a project funded by the [Wellcome Trust](https://wellcome.ac.uk/) created after the finalization of the 1000 Genomes Project in order to maintain and expand the resource. It has the following aims:
+
+        * Ensure the future access to and usability of the 1000 Genomes reference data
+        * Incorporate additional published genomic data on the 1000 Genomes samples
+        * Expand the data collection to include new populations not represented in the 1000 Genomes Project 
+
+        This repository contains code used in the different analyses pipelines that we use in the project. To use this code please follow the steps described below
+
+        ### Preparing environment
+        Modify your $PYTHONPATH to include the required libraries:<br>
+        ```export PYTHONPATH=${ehive_dir}/wrappers/python3/:$PYTHONPATH```
+
+        Modify your $PERL5LIB to include the required libraries:<br>
+        ```export PERL5LIB=${ehive_dir}/modules/:${igsr_analysis_dir}/:${PERL5LIB}```
+
+        Modify your $PATH to include the location of the eHive scripts:
+        ```export PATH=${ehive_dir}/scripts/:${PATH}```
+
+        ### Install the igsr_analysis package from PyPI
+
+        ```pip install igsr_analysis```
+
+        And you are ready to go! 
+
+        ### Conventions used in this README file:
+
+        ```${igsr_analysis_dir}``` is the folder where you have cloned https://github.com/igsr/igsr_analysis.git<br>
+        ```${ehive_dir}``` is the folder where you have cloned https://github.com/Ensembl/ensembl-hive.git<br>
+
+        [![DOI](https://zenodo.org/badge/99792445.svg)](https://zenodo.org/badge/latestdoi/99792445)
+
+Platform: UNKNOWN
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.0
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.0.0
+Description-Content-Type: text/markdown

igsr_analysis.egg-info/SOURCES.txt

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+README.md
+setup.py
+BEDTools/BEDTools.py
+BEDTools/__init__.py
+BamQC/BamQC.py
+BamQC/__init__.py
+PyHive/Hive.py
+PyHive/__init__.py
+PyHive/Attribute/StoreAttribute.py
+PyHive/Attribute/__init__.py
+PyHive/Bam/RunSamToolsIndex.py
+PyHive/Bam/RunSamToolsMerge.py
+PyHive/Bam/__init__.py
+PyHive/BamQC/RunChkIndelRg.py
+PyHive/BamQC/RunPicardOnWESfile.py
+PyHive/BamQC/RunPicardOnWGSfile.py
+PyHive/BamQC/RunVerifyBamId.py
+PyHive/BamQC/__init__.py
+PyHive/Factories/BeagleChunkFactory.py
+PyHive/Factories/ChrFactory.py
+PyHive/Factories/CoordFactory.py
+PyHive/Factories/ShapeitChunkFactory.py
+PyHive/Factories/SliceFactory.py
+PyHive/Factories/SplitVCF.py
+PyHive/Factories/SplitVCFintoChros.py
+PyHive/Factories/TransposeBam.py
+PyHive/Factories/__init__.py
+PyHive/File/CompressBybgzip.py
+PyHive/File/ShortenFilePaths.py
+PyHive/File/ShortenFiles.py
+PyHive/File/SplitFile.py
+PyHive/File/StoreFile.py
+PyHive/File/__init__.py
+PyHive/Seed/SeedFile.py
+PyHive/Seed/SeedShapeit.py
+PyHive/Seed/SeedVCFIntegration.py
+PyHive/Seed/__init__.py
+PyHive/TOPMed/IndexBam.py
+PyHive/TOPMed/MarkDuplicates.py
+PyHive/TOPMed/RnaseqcCounts.py
+PyHive/TOPMed/Rsem.py
+PyHive/TOPMed/SamtoolsQuickcheck.py
+PyHive/TOPMed/Star.py
+PyHive/TOPMed/__init__.py
+PyHive/VariantCalling/BCFTools_caller.py
+PyHive/VariantCalling/GATK_HC.py
+PyHive/VariantCalling/GATK_UG.py
+PyHive/VariantCalling/__init__.py
+PyHive/Vcf/BcftoolsVcfNorm.py
+PyHive/Vcf/CombineVariants.py
+PyHive/Vcf/NormVcf.py
+PyHive/Vcf/VariantsToAllelicPrimitives.py
+PyHive/Vcf/VcfAllelicPrim.py
+PyHive/Vcf/VcfCombine.py
+PyHive/Vcf/VcfConcat.py
+PyHive/Vcf/VcfIxByTabix.py
+PyHive/Vcf/VcfReheader.py
+PyHive/Vcf/VcfReplaceChrNames.py
+PyHive/Vcf/__init__.py
+PyHive/Vcf/convertPL2GL.py
+PyHive/Vcf/dropInfo.py
+PyHive/VcfFilter/ApplyRecalibration.py
+PyHive/VcfFilter/BcftoolsFilter.py
+PyHive/VcfFilter/SelectVariants.py
+PyHive/VcfFilter/SplitVariants.py
+PyHive/VcfFilter/SubsetVcfWithBed.py
+PyHive/VcfFilter/SubsetVcfWithRegion.py
+PyHive/VcfFilter/VariantRecalibrator.py
+PyHive/VcfFilter/__init__.py
+PyHive/VcfIntegration/CollectRawF.py
+PyHive/VcfIntegration/SNPTools_bamodel.py
+PyHive/VcfIntegration/SNPTools_poprob.py
+PyHive/VcfIntegration/SNPTools_prob2vcf.py
+PyHive/VcfIntegration/__init__.py
+PyHive/VcfIntegration/run_Beagle.py
+PyHive/VcfIntegration/run_Shapeit.py
+PyHive/VcfIntegration/run_Shapeit_convert2vcf.py
+PyHive/VcfIntegration/run_ligateHAPLOTYPES.py
+PyHive/VcfIntegration/run_prepareGenFromBeagle4.py
+PyHive/VcfQC/BcftoolsStats.py
+PyHive/VcfQC/ChrosInVcf.py
+PyHive/VcfQC/CollectVariantCallingMetrics.py
+PyHive/VcfQC/GTConcordance.py
+PyHive/VcfQC/PlotVariantDensity.py
+PyHive/VcfQC/VariantsInRegions.py
+PyHive/VcfQC/__init__.py
+ReseqTrackDB/ReseqTrackDB.py
+ReseqTrackDB/__init__.py
+ReseqTrackDB/main.py
+SequenceIndex/SequenceIndex.py
+SequenceIndex/__init__.py
+SequenceIndex/main.py
+Utils/RunProgram.py
+Utils/RunSingularity.py
+Utils/__init__.py
+VCF/VcfNormalize.py
+VCF/VcfQC.py
+VCF/VcfUtils.py
+VCF/__init__.py
+VCF/VCFIntegration/Beagle.py
+VCF/VCFIntegration/SNPTools.py
+VCF/VCFIntegration/Shapeit.py
+VCF/VCFIntegration/__init__.py
+VCF/VCFfilter/BCFTools.py
+VCF/VCFfilter/GATK.py
+VCF/VCFfilter/MLclassifier.py
+VCF/VCFfilter/__init__.py
+VariantCalling/BCFTools.py
+VariantCalling/GATK.py
+VariantCalling/__init__.py
+igsr_analysis.egg-info/PKG-INFO
+igsr_analysis.egg-info/SOURCES.txt
+igsr_analysis.egg-info/dependency_links.txt
+igsr_analysis.egg-info/requires.txt
+igsr_analysis.egg-info/top_level.txt
+p3/__init__.py
+p3/p3BAMQC.py

igsr_analysis.egg-info/dependency_links.txt

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+

igsr_analysis.egg-info/requires.txt

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+pandas

igsr_analysis.egg-info/top_level.txt

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+BEDTools
+BamQC
+PyHive
+ReseqTrackDB
+SequenceIndex
+Utils
+VCF
+VariantCalling
+p3