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nf-core / kmermaid

k-mer similarity analysis pipeline
https://nf-co.re/kmermaid
MIT License
19 stars 12 forks source link

Upgrade tqdm to 4.29.1 for tqdm.auto #50

Closed olgabot closed 4 years ago

olgabot commented 4 years ago

As mentioned here: https://github.com/nteract/papermill/issues/287

Otherwise get this error (from using #48 )

Caused by:
  Process `count_umis_per_cell (ANTOINE_LIVER)` terminated with an error exit status (1)

Command executed:

  count_umis_per_cell.py \
      --reads ANTOINE_LIVER__aligned.fastq.gz \
      --min-umi-per-cell 5001 \
      --cell-barcode-pattern '(CB|CB):Z:([ACGT]+)(\-1)?' \
      --molecular-barcode-pattern '(UB|XB):Z:([ACGT]+)' \
      --umis-per-cell ANTOINE_LIVER__n_umi_per_cell.csv \
      --good-barcodes ANTOINE_LIVER__barcodes.tsv

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/olga/.nextflow/assets/nf-core/kmermaid/bin/count_umis_per_cell.py", line 9, in <module>
      from tqdm.auto import tqdm
  ModuleNotFoundError: No module named 'tqdm.auto'
pranathivemuri commented 4 years ago

https://github.com/nf-core/kmermaid/pull/93