search

jts / ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
47 stars 16 forks source link

PDF reports fails to generate due to missing "lineage_notes" key #69

Closed DarianHole closed 3 years ago

DarianHole commented 3 years ago

Hi everyone,

After the latest update to the pdf report I keep getting a key error for missing the lineage_notes key. For the moment I've gotten it to work by checking out to the commit before this change (01e044b3e56ef2460abf93cf7d475072df23f078).

Error:

rule make_report_tex:
    input: qc_reports/nml_summary_qc.tsv, lineages/nml_pangolin_version.txt, plots/nml_tree_snps.pdf
    output: qc_reports/nml.tex
    jobid: 2
    wildcards: prefix=nml

Traceback (most recent call last):
  File "/ncov-tools/workflow/rules/../scripts/generate_report.py", line 355, in <module>
    write_summary_qc_section()
  File "/ncov-tools/workflow/rules/../scripts/generate_report.py", line 274, in write_summary_qc_section
    tsv_to_table(args.summary_qc_table.format(run_name=args.run_name), tf)
  File "/ncov-tools/workflow/rules/../scripts/generate_report.py", line 95, in tsv_to_table
    del row[k]
KeyError: 'lineage_notes'

Let me know if I've missed anything to easily solve this!

Thanks, Darian

jts commented 3 years ago

This change requires updating the ncov-parser library in the environment to version 0.6.4

DarianHole commented 3 years ago

Ah thanks, I keeping missing those updates