lskatz/SneakerNet

Issues

• colorid dependency

  #71 opened 9 months ago by lskatz
  0

• uuencode dependency

  #69 opened 9 months ago by lskatz
  1

• Troubleshooting workflow

  #65 opened 2 years ago by lskatz
  0

• Documentation for repo structure

  #63 opened 2 years ago by lskatz
  1

• perldoc

  #64 opened 2 years ago by lskatz
  1

• incorrect link on main README for parse sample entries

  #57 opened 2 years ago by kapsakcj
  0

• add badge & short section on JOSS publication

  #60 opened 4 years ago by kapsakcj
  1

• transferFilesToRemoteComputers.pl bug

  #58 opened 4 years ago by kapsakcj
  2

• Detect taxa in parse sample sheet page

  #54 opened 4 years ago by lskatz
  0

• SARS-CoV-2

  #53 opened 4 years ago by lskatz
  1

• SPAdes assembly

  #52 opened 4 years ago by lskatz
  1

• Plasmid plugin

  #51 opened 4 years ago by lskatz
  0

• Need to document assembly workflow

  #49 opened 4 years ago by lskatz
  0

• Consider adding information about compute resources needed

  #42 opened 5 years ago by lfaller
  7

• Please consider fully moving to docker for installation purposes

  #41 opened 5 years ago by lfaller
  5

• Warnings for MLST

  #46 opened 5 years ago by lskatz
  0

• Warnings/errors expansion

  #32 opened 5 years ago by lskatz
  0

• Cleaned reads plugin

  #45 opened 5 years ago by lskatz
  1

• discuss available resources

  #44 opened 5 years ago by lskatz
  1

• pass/fail to include 7-gene MLST?

  #25 opened 5 years ago by lskatz
  1

• Pipeline does not exit gracefully if sample files are listed in sample sheet but no FASTQ data is present

  #40 opened 5 years ago by lfaller
  3

• Does the --parsesamplesheet option still exist?

  #39 opened 5 years ago by lfaller
  1

• Please complete the Apache license copyright field

  #38 opened 5 years ago by lfaller
  1

• Kraken is too sensitive for calling contamination

  #34 opened 5 years ago by lskatz
  2

• Documentation for new organisms

  #36 opened 5 years ago by lskatz
  1

• Switch to Fasten from CG-Pipeline in a future version of SneakerNet

  #37 opened 5 years ago by lskatz
  0

• Need unit testing

  #23 opened 5 years ago by lskatz
  1

• Bash hello world example not conforming

  #33 opened 5 years ago by lskatz
  1

• colorid not checked in dependency checking scripts

  #27 opened 5 years ago by kapsakcj
  5

• bcl2fastq missed

  #30 opened 5 years ago by kapsakcj
  2

• Docker init

  #28 opened 5 years ago by lskatz
  6

• Separate out Kraken analysis from Kraken results

  #18 opened 5 years ago by lskatz
  1

• Better dependency descriptions in scripts

  #22 opened 5 years ago by lskatz
  1

• Method to add warnings

  #26 opened 5 years ago by lskatz
  2

• Add Salmonella genome to test set

  #24 opened 5 years ago by lskatz
  1

• 18S plugin

  #13 opened 5 years ago by lskatz
  1

• Pointfinder

  #21 opened 5 years ago by lskatz
  1

• Perl5doc needed for sneakernet.pm

  #20 opened 5 years ago by lskatz
  1

• The kraken failure should be moved to sn_passfail.pl

  #19 opened 5 years ago by lskatz
  1

• Kraken should look at contigs if reads are not present

  #17 opened 5 years ago by lskatz
  1

• Documentation for samples.tsv

  #16 opened 5 years ago by lskatz
  1

• Plugin for wgMLST

  #11 opened 5 years ago by lskatz
  1

• ANI species plugin

  #10 opened 5 years ago by lskatz
  1

• GP60

  #12 opened 5 years ago by lskatz
  1

• Script to check for prerequisites

  #14 opened 5 years ago by lskatz
  5

• Main documentation

  #15 opened 5 years ago by lskatz
  2

• Need a documentation logo in the report

  #9 opened 5 years ago by lskatz
  1

• Citation needed

  #6 opened 6 years ago by lskatz
  0

• Plugins showcase

  #7 opened 6 years ago by lskatz
  0

• Switch to Skesa assembler in assembly plugin

  #2 opened 7 years ago by lskatz
  1