broadinstitute/funpipe issues and pull requests

#65 - Bump setuptools from 65.6.3 to 70.0.0

Pull Request - State: open - Opened by dependabot[bot] 2 months ago
Labels: dependencies

#64 - refact: add utility tool to enable direct run of funpipe modules

Issue - State: open - Opened by xiaoli0 9 months ago

#63 - refact: update OOP modules using FILE

Issue - State: open - Opened by xiaoli0 9 months ago
Labels: enhancement

#62 - feat: add FILE base object for all formats

Issue - State: open - Opened by xiaoli0 9 months ago
Labels: enhancement

#61 - docs: update README to latest version

Issue - State: open - Opened by xiaoli0 9 months ago

#60 - Bump numpy from 1.15.4 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#59 - Update sphinx doc style

Pull Request - State: open - Opened by xiaoli0 over 1 year ago

#58 - Installation - Please make sure you have the correct access rights

Issue - State: closed - Opened by ariasamin about 2 years ago - 1 comment

#57 - add gaemr to pypi and conda env

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#56 - docker image to google contain registry

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#55 - python version test badge

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#54 - coverall badge

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#53 - release newly updated version to pypi

Issue - State: closed - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#52 - Parse genotype concordance output

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#51 - Add GEMMA analysis pipeline for GWAS analysis

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#50 - Add popgenome analysis

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#49 - packaging and distributing via pypi

Issue - State: closed - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#48 - publication

Issue - State: open - Opened by xiaoli0 over 5 years ago

#47 - Include examples in documentation

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#46 - coverage_plot.py clustering update

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#45 - Update variable names: cov_tsv referred to different files

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#44 - coverage_plot.py test_get_contig_sets bug

Issue - State: closed - Opened by xiaoli0 over 5 years ago - 1 comment
Labels: bugs

#43 - replace coverage_barplot.R with covisr package

Issue - State: open - Opened by xiaoli0 over 5 years ago

#42 - add option of coverage_analysis.py for project directory

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#41 - replace R scripts

Issue - State: open - Opened by xiaoli0 over 5 years ago
Labels: low priority

#40 - Implement a data manager functionality that reflects how firehose/firecloud manage data

Issue - State: closed - Opened by xiaoli0 over 5 years ago
Labels: enhancement

#39 - automate qc metr plot

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#38 - remove default local jars

Issue - State: closed - Opened by xiaoli0 almost 6 years ago
Labels: bugs

#37 - docker use GATK4

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#36 - add readthedoc

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#35 - incorporate legacy tool

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#34 - Env setting docs + conda

Pull Request - State: closed - Opened by xiaoli0 almost 6 years ago

#33 - biolego gitter channel

Issue - State: closed - Opened by xiaoli0 almost 6 years ago

#32 - add mating type analysis to the pipeline

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#31 - work with compressed VCFs

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement, low priority

#30 - fully setup readdoc

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement, low priority

#29 - test filter_gatk_genotypes.py

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#28 - unit tests for vcfTools.py

Issue - State: open - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#27 - Aneuploidy analysis

Pull Request - State: closed - Opened by xiaoli0 almost 6 years ago

#26 - add vcf analysis functions

Pull Request - State: closed - Opened by xiaoli0 almost 6 years ago
Labels: enhancement

#25 - visualize pct chr covered by violin plot

Issue - State: open - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#24 - coverage_analysis.py pct contig coverage

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#23 - travis automatic deployment

Issue - State: open - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#22 - coverage_analysis.py add subgenome pct plot

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#21 - snpeff in python

Issue - State: open - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#20 - coverage_analysis.py get aneuploidy proportion

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#19 - add cutoff option to coverage_plot.R

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#18 - bam_qc_metr.py parse sample name wrong

Issue - State: closed - Opened by xiaoli0 about 6 years ago

#17 - add scripts for picard qc bam

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#16 - automate coverage_analysis.py to include plot script

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#15 - automate coverage R plot

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#14 - Improve sphinx automatic doc generation

Issue - State: open - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#13 - WDL for automation

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#12 - Make python package

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#11 - dockerize environment

Issue - State: open - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#10 - add cnvotator function to pipeline

Issue - State: open - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#9 - dep_per_win.pl illegal devision

Issue - State: closed - Opened by xiaoli0 about 6 years ago - 1 comment

#8 - Add progress report

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#7 - Setup tool installation for ease of use

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#6 - Add breakdancer functionality

Issue - State: open - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#5 - test submitting jobs with python

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#4 - Add options to take in json file as input to all tools

Issue - State: closed - Opened by xiaoli0 about 6 years ago - 1 comment
Labels: enhancement, wontfix

#3 - run_ploidy.py take in fasta rather than fai

Issue - State: closed - Opened by xiaoli0 about 6 years ago
Labels: enhancement

#2 - Improve performance of `run_ploidy.py`.

Issue - State: closed - Opened by xiaoli0 over 6 years ago
Labels: enhancement

#1 - dep_per_win.pl not deal with end of chromosomes correctly

Issue - State: open - Opened by xiaoli0 over 6 years ago - 1 comment
Labels: low priority

GitHub / broadinstitute/funpipe issues and pull requests