shandley/hecatomb

Issues

• Problem with running

  #46 opened 3 years ago
  11

• does --configfile work with the download script?

  #45 opened 3 years ago
  1

• settings in '--configfile' file not passed to 'script:' rules

  #44 opened 2 years ago
  1

• Hecatomb v1.0.0.beta.2 crash

  #43 opened 3 years ago
  2

• updating hecatomb

  #40 opened 3 years ago
  1

• kill switch

  #39 opened 3 years ago
  1

• mouse

  #38 opened 3 years ago
  1

• Error in rule PRIMARY_NT_reformat

  #37 opened 3 years ago
  4

• pipeline requires higher version of conda which has --conda-frontend parameter

  #36 opened 3 years ago
  3

• hecatomb's same output files from the same dataset are with different sizes

  #35 opened 3 years ago
  10

• missing python package

  #34 opened 3 years ago
  1

• megahit -> flye reformatting

  #29 opened 3 years ago
  1

• For NextSeq samples, maximum HTCF memory insufficient for merge seqtable step in R

  #28 opened 3 years ago
  1

• flye "Looks like the system ran out of memory"

  #27 opened 4 years ago
  3

• two concerns with the convert_phyloseq_euk_viral_glom.r standardized count table (species)

  #26 opened 2 years ago
  0

• WorkflowError in line 122 of 01_contaminant_removal_hosts.smk: Resources function did not return int.

  #25 opened 3 years ago
  1

• the "Running on Slurm" part in the INSTALLATION.md file has an extra space in parameter -o

  #24 opened 3 years ago
  0

• Update phage lineages

  #23 opened 3 years ago
  0

• Streamline file zipping and unzipping

  #22 opened 3 years ago
  0

• Streamline fastq vs fasta file usage

  #21 opened 3 years ago
  0

• additional script to merge new data with old at seqtable_merge.R level

  #20 opened 2 years ago
  3

• convert_phyloseq.R

  #19 opened 3 years ago
  1

• How to convert fastq-dumps to R1 /R2

  #18 opened 3 years ago
  0

• Mappers for host removal

  #17 opened 3 years ago
  0

• Update mmseqs scripts to work with the newest version of mmseqs2

  #16 opened 3 years ago
  0

• Update download databases for bowtie2

  #14 opened 4 years ago
  0

• Add human taxonomy to a taxtable

  #13 opened 4 years ago
  0

• Error downloading databases

  #12 opened 3 years ago
  5

• include info about potential false positives in README?

  #11 opened 3 years ago
  3

• read pair handling

  #10 opened 3 years ago
  2

• slurm and space

  #9 opened 4 years ago
  0

• Create a new release

  #8 opened 4 years ago
  1

• Update master to Rob's branch

  #7 opened 4 years ago
  1

• Make primerB heat map

  #6 opened 4 years ago
  1

• Find R1 and R2 for multiple samples

  #4 opened 4 years ago
  2