aryarm/as_analysis issues and pull requests

#79 - Specify in docs that vcf file needs accompanying index file

Issue - State: open - Opened by zrcjessica almost 4 years ago - 1 comment

#78 - document meaning of columns in output of R scripts

Issue - State: open - Opened by aryarm almost 4 years ago

#77 - add config option for supporting reads cutoff

Issue - State: open - Opened by aryarm almost 4 years ago
Labels: enhancement

#76 - start on work for asoc analysis

Pull Request - State: closed - Opened by aryarm almost 4 years ago

#75 - priorities

Issue - State: open - Opened by aryarm almost 4 years ago

#74 - big picture: turning this into a command line tool

Issue - State: open - Opened by aryarm almost 4 years ago - 1 comment
Labels: enhancement

#73 - create a small, test dataset and a testing suite

Issue - State: open - Opened by aryarm about 4 years ago - 2 comments
Labels: enhancement, good first issue

#72 - simplify how samples are specified

Issue - State: open - Opened by aryarm about 4 years ago - 4 comments
Labels: enhancement

#71 - allow BAM files as input to the WASP subworkflow

Issue - State: open - Opened by aryarm about 4 years ago - 1 comment
Labels: enhancement, gcp

#70 - Change name of column for proportion of ref allele in rna.csv.gz

Issue - State: open - Opened by zrcjessica about 4 years ago

#69 - add support for peak regions for ASOC analysis

Issue - State: open - Opened by zrcjessica about 4 years ago - 2 comments

#68 - add error messages for dataframes with 0 rows after filtering

Issue - State: open - Opened by zrcjessica about 4 years ago - 1 comment

#67 - remove quoting in CSVs output by R scripts

Issue - State: open - Opened by aryarm about 4 years ago
Labels: enhancement

#66 - support for unpaired reads in the WASP subworkflow

Pull Request - State: open - Opened by aryarm about 4 years ago

#65 - support for single-end RNA-seq and ATAC-seq in the WASP subworkflow

Issue - State: open - Opened by aryarm about 4 years ago
Labels: enhancement

#64 - allow gzipped FASTAs and GTFs when using STAR

Issue - State: open - Opened by aryarm about 4 years ago - 1 comment
Labels: enhancement

#63 - extract heterozygotes from the vcf before converting to h5 files

Issue - State: open - Opened by aryarm about 4 years ago - 1 comment
Labels: enhancement

#62 - preliminary support for allele specific open chromatin (ASOC) analyses

Pull Request - State: closed - Opened by aryarm about 4 years ago
Labels: enhancement

#61 - ATAC-seq support

Issue - State: open - Opened by aryarm over 4 years ago - 1 comment
Labels: enhancement

#60 - assume GQ = 20 in the absence of GQ tags within the provided VCF

Issue - State: closed - Opened by aryarm over 4 years ago
Labels: enhancement

#59 - filter to only GQ tag before extracting GQ tags per sample

Issue - State: open - Opened by aryarm over 4 years ago
Labels: enhancement, gcp

#58 - set disk_mb values appropriately

Issue - State: open - Opened by aryarm over 4 years ago
Labels: bug, gcp

#57 - allow for linking samples from a terra bucket

Issue - State: open - Opened by aryarm over 4 years ago - 2 comments
Labels: enhancement, gcp

#56 - improve dependency installation on cloud

Issue - State: open - Opened by aryarm over 4 years ago
Labels: enhancement, gcp

#55 - preemptible instances

Issue - State: open - Opened by aryarm over 4 years ago
Labels: enhancement, gcp

#54 - allow input as h5 files

Issue - State: closed - Opened by aryarm over 4 years ago - 1 comment
Labels: enhancement

#53 - skipping the variant calling pipeline within the master pipeline

Issue - State: closed - Opened by aryarm over 4 years ago - 1 comment
Labels: enhancement

#52 - check samples exist

Issue - State: closed - Opened by aryarm over 5 years ago - 1 comment

#51 - use checkpoints instead of dynamic

Issue - State: closed - Opened by aryarm over 5 years ago - 1 comment

#50 - snps that don't overlap a gene

Issue - State: open - Opened by aryarm over 5 years ago - 1 comment
Labels: bug

#49 - LD_LIBRARY_PATH problems

Issue - State: open - Opened by aryarm over 6 years ago - 2 comments
Labels: bug

#48 - consider extracting common rules to separate snakefile

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

#47 - r packages

Issue - State: open - Opened by aryarm over 6 years ago
Labels: enhancement

#46 - extracting heterozygotes in rules.extract_hets

Issue - State: closed - Opened by aryarm over 6 years ago
Labels: bug

#45 - a report

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

#44 - download WASP for the user

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#43 - re-attempt failed jobs and scale resource usage

Issue - State: closed - Opened by aryarm over 6 years ago - 2 comments
Labels: enhancement

#42 - improve use of STAR in Snakefile-WASP

Issue - State: closed - Opened by aryarm over 6 years ago

#41 - update default env to reflect new WASP version

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#40 - rna version of allele.imbalance script

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#39 - consider printing progress statements in prepare_counts and find_imbalance?

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

#38 - prepare_counts uses too much memory

Issue - State: closed - Opened by aryarm over 6 years ago - 5 comments

#37 - revise params

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

#36 - use of samples file prevents reruns

Issue - State: closed - Opened by aryarm over 6 years ago

#35 - memory

Issue - State: closed - Opened by aryarm over 6 years ago - 2 comments
Labels: enhancement

#34 - modify our use of WASP snakemake pipeline to save space

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment

#33 - SNPs only

Issue - State: closed - Opened by aryarm over 6 years ago - 2 comments
Labels: bug

#32 - incorporate R package dependencies into default conda env

Issue - State: closed - Opened by aryarm over 6 years ago
Labels: enhancement, good first issue

#31 - parallelize R script

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

#30 - extract hets from WASP counts, as well

Issue - State: closed - Opened by aryarm over 6 years ago
Labels: bug

#29 - extract gq into one file

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#28 - switch to tsv's

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

#27 - gzip all of the things

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#26 - investigate heterozygotes in counts data

Issue - State: closed - Opened by aryarm over 6 years ago

#25 - add vqsr filtering for indels?

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment

#24 - set min snakemake version

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

#23 - clean up repo

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment

#22 - rewrite config files to take advantage of yaml

Issue - State: closed - Opened by aryarm over 6 years ago - 3 comments
Labels: enhancement

#21 - incorporate hard filtering into variant calling pipeline

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

#20 - use wildcards to get_as_counts dna/rna

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

#19 - samtools mutli threading

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

#18 - provide flexibility for specifying samples

Issue - State: closed - Opened by aryarm over 6 years ago - 5 comments
Labels: enhancement, good first issue

#17 - include index files in all rules

Issue - State: closed - Opened by aryarm over 6 years ago

#16 - refine python code in Snakefiles

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

#15 - redevelop find_imbalance.r for multiple samples

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment

#14 - running entire pipeline all at once

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#13 - shadow rules

Issue - State: closed - Opened by aryarm over 6 years ago - 4 comments
Labels: enhancement

#12 - split Snakefile

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment

#11 - specifying specific samples

Issue - State: closed - Opened by aryarm over 6 years ago
Labels: bug

#10 - incorporate R script into Snakefile

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment

#9 - incorporate WASP pipeline back into Snakefile

Issue - State: closed - Opened by aryarm over 6 years ago

#8 - test final.bash equivalent of snakemake pipeline

Issue - State: closed - Opened by aryarm over 6 years ago
Labels: good first issue

#7 - create config option for base score and variant score recalibration

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#6 - named pipes

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: bug, enhancement

#5 - use snakemake validation

Issue - State: open - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#4 - reference genome index files

Issue - State: open - Opened by aryarm over 6 years ago - 4 comments
Labels: enhancement

#3 - multi-threading for gatk

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#2 - conda envs

Issue - State: closed - Opened by aryarm over 6 years ago - 1 comment
Labels: enhancement

#1 - wasp mode of STAR

Issue - State: closed - Opened by aryarm over 6 years ago - 3 comments

GitHub / aryarm/as_analysis issues and pull requests