SaundersLab/marple-pst

Issues

• line 3: xml_catalog_files_libxml2: unbound variable

  #43 opened a year ago
  0

• reads_to_exons_concat crashes if there are no SNPs

  #41 opened 2 years ago
  0

• installer crashes if curl not installed

  #40 opened 2 years ago
  0

• add percentage of positions to multiqc report

  #38 opened 2 years ago
  0

• can we drop requirement for 20x at a SNP if we've seen that base in other isolates?

  #37 opened 2 years ago
  0

• verify RAxML model choice

  #36 opened 2 years ago
  0

• investigate haplotype identification tools

  #35 opened 2 years ago
  0

• Norfolk-1 example FASTQ file not valid

  #34 opened 2 years ago
  0

• Add PST-130 to the tree

  #33 opened 2 years ago
  0

• Its 57 isolates not 56

  #32 opened 2 years ago
  0

• reset example won't work on HPC

  #31 opened 2 years ago
  0

• --version should print the version name

  #30 opened 2 years ago
  0

• add amplimer coverage calculations

  #29 opened 2 years ago
  1

• add linguist-generated to exclude HTML from GitHub language calculation

  #28 opened 2 years ago
  0

• add trimming

  #27 opened 2 years ago
  0

• reduce file sizes

  #26 opened 2 years ago
  0

• speed up pileup creation

  #25 opened 2 years ago
  1

• cannot use SLURM sbatch for reads_to_exons_concat.sh or exons_concat_to_tree_imgs.sh or sbatch

  #24 opened 2 years ago
  0

• gene coverage axis labels wrong in MultiQC report

  #23 opened 2 years ago
  0

• FASTQC report is not made if the fastq is compressed

  #22 opened 2 years ago
  0

• pipeline crashes in parallel because indexing the reference intereferes with each other

  #21 opened 2 years ago
  1

• sample report does not work unless the sample name matches the directory name

  #20 opened 2 years ago
  0

• Add ET08 PstS6 to the tree input

  #19 opened 2 years ago
  1

• threads flag not handled properly

  #18 opened 2 years ago
  1

• add flag for Porechop

  #17 opened 2 years ago
  0

• GUI

  #16 opened 2 years ago
  0

• add tool for doing the sample renaming

  #15 opened 2 years ago
  1

• screencast for running the pipeline

  #14 opened 2 years ago
  0

• add logging

  #13 opened 2 years ago
  0

• discrepancy in coverage calculation between old and new pipeline

  #12 opened 2 years ago
  0

• rename samples in newick file

  #11 opened 2 years ago
  1

• off by one error in snp_ratios_and_snp_freq_to_consensus line 80

  #10 opened 2 years ago
  0

• newick file creation test is too specific

  #9 opened 2 years ago
  1

• strange tar messages when running example

  #8 opened 2 years ago
  1

• installer does not work on WSL

  #7 opened 2 years ago
  1

• prompt user if marple-pst already exists instead of just overwriting it

  #6 opened 2 years ago
  0

• use mamba instead of conda

  #5 opened 2 years ago
  2

• Allow user to specify threads for reads_to_exons_concat

  #4 opened 2 years ago
  0

• Add GitHub action to run tests and update code coverage

  #3 opened 2 years ago
  1

• Cover all of example with tests

  #2 opened 2 years ago
  1

• Update installer and test on M1 machine

  #1 opened 2 years ago
  0