Issues

• Non-indexed Mode

  enhancement
  jhuapl-bio/basestack_consensus#50 · Filter by author Merritt-Brian opened on Aug 2, 2021

• Permission denied OR Command Error non-fastq files in fastq folder(s) in Module 4

  bug
  jhuapl-bio/basestack_consensus#49 · Filter by author Merritt-Brian opened on Apr 29, 2021
  1

• Ignore Misnamed or Extra Barcodes

  enhancementquestion
  jhuapl-bio/basestack_consensus#48 · Filter by author Merritt-Brian opened on Apr 29, 2021

• pool figures run off page

  jhuapl-bio/basestack_consensus#46 · Filter by author tmehoke opened on Mar 25, 2021

• awk is unstable in some places between mawk and gawk

  jhuapl-bio/basestack_consensus#41 · Filter by author tmehoke opened on Mar 4, 2021

• check issues with using relative path instead of absolute path

  jhuapl-bio/basestack_consensus#31 · Filter by author tmehoke opened on Feb 19, 2021

• flu primer scheme BED files need to be named correctly

  jhuapl-bio/basestack_consensus#30 · Filter by author tmehoke opened on Feb 19, 2021

• manage pipeline in central Makefile

  jhuapl-bio/basestack_consensus#28 · Filter by author tmehoke opened on Feb 19, 2021

• nextstrain not installed in image

  jhuapl-bio/basestack_consensus#26 · Filter by author tmehoke opened on Feb 18, 2021

• FASTQ files are fully duplicated through FASTQ, SAM, and BAM files in modules 1, 2, and 3

  jhuapl-bio/basestack_consensus#22 · Filter by author tmehoke opened on Feb 17, 2021
  

• don't assume NB barcodes in manifest file for module 1

  jhuapl-bio/basestack_consensus#18 · Filter by author tmehoke opened on Jan 22, 2021
  1

  

• relax 'No' flag to allow more detailed inspection of 'Maybe' flags

  jhuapl-bio/basestack_consensus#15 · Filter by author tmehoke opened on Jan 11, 2021

• add an argument to receive the selected fastq directory into module 1

  jhuapl-bio/basestack_consensus#14 · Filter by author tmehoke opened on Jan 8, 2021

• demux all possible barcodes in step 1

  jhuapl-bio/basestack_consensus#8 · Filter by author tmehoke opened on Jan 4, 2021

• add outer wrapper for steps 2-4 to run through all samples in manifest

  jhuapl-bio/basestack_consensus#7 · Filter by author tmehoke opened on Jan 4, 2021

• check barcode mismatch in demux step

  jhuapl-bio/basestack_consensus#1 · Filter by author tmehoke opened on Dec 31, 2020
  1