aryarm/as_analysis

Issues

• LD_LIBRARY_PATH problems

  #49 opened 6 years ago by aryarm
  2

• create a small, test dataset and a testing suite

  #73 opened 4 years ago by aryarm
  2

• simplify how samples are specified

  #72 opened 4 years ago by aryarm
  4

• big picture: turning this into a command line tool

  #74 opened 4 years ago by aryarm
  1

• priorities

  #75 opened 4 years ago by aryarm
  0

• Specify in docs that vcf file needs accompanying index file

  #79 opened 4 years ago by zrcjessica
  1

• document meaning of columns in output of R scripts

  #78 opened 4 years ago by aryarm
  0

• set disk_mb values appropriately

  #58 opened 4 years ago by aryarm
  0

• add support for peak regions for ASOC analysis

  #69 opened 4 years ago by zrcjessica
  2

• allow for linking samples from a terra bucket

  #57 opened 4 years ago by aryarm
  2

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

  #65 opened 4 years ago by aryarm
  0

• add config option for supporting reads cutoff

  #77 opened 4 years ago by aryarm
  0

• allow BAM files as input to the WASP subworkflow

  #71 opened 4 years ago by aryarm
  1

• ATAC-seq support

  #61 opened 4 years ago by aryarm
  1

• allow gzipped FASTAs and GTFs when using STAR

  #64 opened 4 years ago by aryarm
  1

• add error messages for dataframes with 0 rows after filtering

  #68 opened 4 years ago by zrcjessica
  1

• snps that don't overlap a gene

  #50 opened 6 years ago by aryarm
  1

• Change name of column for proportion of ref allele in rna.csv.gz

  #70 opened 4 years ago by zrcjessica
  0

• remove quoting in CSVs output by R scripts

  #67 opened 4 years ago by aryarm
  0

• extract heterozygotes from the vcf before converting to h5 files

  #63 opened 4 years ago by aryarm
  1

• assume GQ = 20 in the absence of GQ tags within the provided VCF

  #60 opened 4 years ago by aryarm
  0

• improve dependency installation on cloud

  #56 opened 4 years ago by aryarm
  0

• filter to only GQ tag before extracting GQ tags per sample

  #59 opened 4 years ago by aryarm
  0

• preemptible instances

  #55 opened 4 years ago by aryarm
  0

• revise params

  #37 opened 4 years ago by aryarm
  0

• skipping the variant calling pipeline within the master pipeline

  #53 opened 4 years ago by aryarm
  1

• check samples exist

  #52 opened 4 years ago by aryarm
  1

• use checkpoints instead of dynamic

  #51 opened 4 years ago by aryarm
  1

• consider extracting common rules to separate snakefile

  #48 opened 4 years ago by aryarm
  0

• allow input as h5 files

  #54 opened 4 years ago by aryarm
  1

• a report

  #45 opened 5 years ago by aryarm
  0

• download WASP for the user

  #44 opened 6 years ago by aryarm
  1

• incorporate R package dependencies into default conda env

  #32 opened 6 years ago by aryarm
  0

• r packages

  #47 opened 6 years ago by aryarm
  0

• re-attempt failed jobs and scale resource usage

  #43 opened 6 years ago by aryarm
  2

• extracting heterozygotes in rules.extract_hets

  #46 opened 6 years ago by aryarm
  0

• improve use of STAR in Snakefile-WASP

  #42 opened 7 years ago by aryarm
  0

• update default env to reflect new WASP version

  #41 opened 7 years ago by aryarm
  1

• rna version of allele.imbalance script

  #40 opened 7 years ago by aryarm
  1

• memory

  #35 opened 7 years ago by aryarm
  2

• consider printing progress statements in prepare_counts and find_imbalance?

  #39 opened 7 years ago by aryarm
  0

• prepare_counts uses too much memory

  #38 opened 7 years ago by aryarm
  5

• gzip all of the things

  #27 opened 7 years ago by aryarm
  1

• extract gq into one file

  #29 opened 7 years ago by aryarm
  1

• use of samples file prevents reruns

  #36 opened 7 years ago by aryarm
  0

• parallelize R script

  #31 opened 7 years ago by aryarm
  0

• SNPs only

  #33 opened 7 years ago by aryarm
  2

• extract hets from WASP counts, as well

  #30 opened 7 years ago by aryarm
  0

• modify our use of WASP snakemake pipeline to save space

  #34 opened 7 years ago by aryarm
  1

• switch to tsv's

  #28 opened 7 years ago by aryarm
  0