epi2me-labs/wf-metagenomics

Issues

• How to export diversity table?

  #69 opened a year ago
  2

• Extract automatically CSV of abundances

  #68 opened a year ago
  5

• html report

  #67 opened a year ago
  4

• Error executing process > 'kraken_pipeline:makeReport

  #66 opened a year ago
  6

• amplicon-seq analysis with ncbi_16s_18s_28s_ITS

  #65 opened a year ago
  1

• wf-metagenomic: Minimap error 16S_18S NCBI database

  #64 opened a year ago
  13

• wf-metagenomics-report

  #63 opened a year ago
  21

• ELPI2ME - DOCKER - Error

  #62 opened a year ago
  12

• Viruses with minimap pipeline

  #61 opened a year ago
  4

• Support directory of sample FASTQs

  #60 opened a year ago
  2

• Workflow hangs

  #59 opened a year ago
  5

• `fastcat` on docker, Segmentation fault

  #58 opened a year ago
  3

• Input path test_data does not exist.

  #57 opened a year ago
  1

• Big ref2taxid.targloci.tsv

  #56 opened a year ago
  2

• ERROR ~ Error executing process > 'kraken_pipeline:run_common:abricateVersion'

  #55 opened 2 years ago
  1

• [Question]: Confidence Parameters for Kraken2 and Bracken

  #54 opened a year ago
  8

• [Bug]:

  #53 opened a year ago
  18

• [bug]: NOTE: Process 'kraken_pipeline:kraken_server' terminated with an error exit status (65) -- Error is ignored.

  #52 opened 2 years ago
  12

• [Bug]: kraken_pipeline:kraken_server terminated

  #51 opened 2 years ago
  3

• [Bug]: Pipeline seems to get stuck at kraken_server/kraken_client

  #50 opened 2 years ago
  3

• [Bug]: /bin/bash: .command.run: No such file or directory

  #49 opened a year ago
  4

• [Bug]: Cannot run epi2me-labs/wf-metagenomics offline

  #48 opened a year ago
  4

• [Bug]:

  #47 opened 2 years ago
  2

• [Bug]: Error executing process > 'minimap_pipeline:minimap (1)

  #46 opened a year ago
  8

• [ETC]: Implanting BLAST instead minimap2 in wf-metagenomics pipeline.

  #45 opened 2 years ago
  1

• [Bug]: How to specify Bracken length

  #44 opened a year ago
  1

• [Bug]: Permission denied, I have tried almost everything from another similar issue, also tried to give permissions using chmod, didn't work.

  #43 opened 2 years ago
  20

• [Bug]: Kraken Pipeline Make Report Terminated with Error

  #42 opened 2 years ago
  2

• [Bug]: Include ".kraken2.assignments.tsv" in the output folder.

  #41 opened a year ago
  5

• [Bug]: wf-metagenomics keeps failing

  #40 opened 2 years ago
  4

• [Bug]: No output file with classified and unclassified reads

  #39 opened a year ago
  3

• [Bug]: Automatic finding of barcoded files not working when using minimap2 classifier

  #38 opened 2 years ago
  4

• Permission Denied

  #37 opened 2 years ago
  5

• [Bug]: Numpy version

  #36 opened 2 years ago
  2

• [Bug]: `--threads` option triggers a bug

  #35 opened 2 years ago
  3

• [Bug]: The README doesn't state how the database has been built

  #34 opened 2 years ago
  3

• [Bug]: Watchmode error in makeReport

  #33 opened a year ago
  6

• Minimap2 usage

  #32 opened 2 years ago
  7

• [Bug]: kraken2-client fails to connect to kraken2-server

  #31 opened 2 years ago
  1

• [Bug]: No such variable: recursion

  #30 opened 2 years ago
  5

• Implement memory-mapping kraken2 option

  #29 opened a year ago
  1

• I just had the `--threads` error too. I used to run the workflow with `--threads 24`. Today I updated to the newest version and its not working anymore.

  #28 opened 2 years ago
  1

• flag for sample_sheet does not work.

  #27 opened a year ago
  6

• [Bug]: workflow fails when more 28 fastq files are being analyzed

  #26 opened 2 years ago
  2

• [Bug]: error while aggregating kraken report with bracken

  #24 opened 2 years ago
  4

• [Bug]: kraken2_client fails with the test data. Server is error state. Return code 12

  #23 opened a year ago
  6

• Barcode02 in test data produces a lot of unclassified reads

  #22 opened 2 years ago
  7

• Barcode02 in test data produces a lot of unclassified reads

  #21 opened 2 years ago
  1

• Permission issue

  #20 opened 2 years ago
  11

• [Bug]: Error: unknown lineage Lu

  #19 opened 2 years ago
  10