Regression in header parsing

[mattheww95]

Description of the bug

Kraken2 report outputs are no longer parsed properly for use in reporting.

A relevant log message is attached below:

Aug-16 12:59:04.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: MIKROKONDO:POST_ASSEMBLY:LOCIDEX:LOCIDEX_SUMMARIZE (test_vibrio); status: COMPLETED; exit: -; error: java.io.FileNotFoundException: /nextflow-scratch-kcochran/mikro_loci8/work/73/b111d581028ae6c6d0315acadd0960/test_vibrio.profile.mlst.json.gz (No such file or directory); workDir: az://nextflow-scratch-kcochran/mikro_loci8/work/60/a1f817affafc5485604d5aeaa840fb]
Aug-16 12:59:04.676 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=MIKROKONDO:POST_ASSEMBLY:LOCIDEX:LOCIDEX_SUMMARIZE (test_vibrio); work-dir=az://nextflow-scratch-kcochran/mikro_loci8/work/60/a1f817affafc5485604d5aeaa840fb
  error [nextflow.exception.ProcessFailedException]: Process `MIKROKONDO:POST_ASSEMBLY:LOCIDEX:LOCIDEX_SUMMARIZE (test_vibrio)` failed
Aug-16 12:59:04.680 [TaskFinalizer-3] INFO  nextflow.processor.TaskProcessor - [60/a1f817] NOTE: Process `MIKROKONDO:POST_ASSEMBLY:LOCIDEX:LOCIDEX_SUMMARIZE (test_vibrio)` failed -- Error is ignored
Aug-16 12:59:04.721 [Actor Thread 24] DEBUG nextflow.util.HashBuilder - [WARN] Unknown hashing type: class _nf_config_3a1f0a2c$_run_closure1$_closure27$_closure68
Aug-16 12:59:04.787 [Actor Thread 24] DEBUG nextflow.util.HashBuilder - [WARN] Unknown hashing type: class _nf_config_3a1f0a2c$_run_closure1$_closure12$_closure63
Aug-16 12:59:05.002 [Task submitter] INFO  nextflow.Session - [59/697ef5] Submitted process > MIKROKONDO:REPORT (Report Generation)
Aug-16 12:59:05.437 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: MIKROKONDO:REPORT (Report Generation); status: COMPLETED; exit: -; error: java.lang.Exception: Mismatched number of passed headers [PercentID, FragmentsRecovered, FragmentsAssignmentTaxon, RankCode] and column values [100.00, 10, 0, R, 1, root] for file /nextflow-scratch-kcochran/mikro_loci8/work/7a/2c5f60c46b51ce08bdf9cfa193ee7d/test_vibrio.kraken2.report.txt; workDir: az://nextflow-scratch-kcochran/mikro_loci8/work/59/697ef50253933523db37cf6ea35b9d]
Aug-16 12:59:05.438 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=MIKROKONDO:REPORT (Report Generation); work-dir=az://nextflow-scratch-kcochran/mikro_loci8/work/59/697ef50253933523db37cf6ea35b9d
  error [nextflow.exception.ProcessFailedException]: Process `MIKROKONDO:REPORT (Report Generation)` failed
Aug-16 12:59:05.451 [TaskFinalizer-4] ERROR nextflow.processor.TaskProcessor - Error executing process > 'MIKROKONDO:REPORT (Report Generation)'

Caused by:
  Mismatched number of passed headers [PercentID, FragmentsRecovered, FragmentsAssignmentTaxon, RankCode] and column values [100.00, 10, 0, R, 1, root] for file /nextflow-scratch-kcochran/mikro_loci8/work/7a/2c5f60c46b51ce08bdf9cfa193ee7d/test_vibrio.kraken2.report.txt -- Check script './modules/local/report.nf' at line: 835

Command used and terminal output

No response

Relevant files

No response

System information

No response

[mattheww95]

addressed in PR #96

[mattheww95]

fixed in: #96