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gatk4/genotypegvcfs tests fail

Open edmundmiller opened this issue 3 years ago • 0 comments

Follow up to #1405

 ───────┬────────────────────────────────────────────────────────────────────────
       │ File: /home/runner/pytest_workflow_swc64_9s/gatk4_genotypegvcfs_test_gatk4_genotypegvcfs_gendb_input/log.out
───────┼────────────────────────────────────────────────────────────────────────
   1   │ N E X T F L O W  ~  version 21.10.6
   2   │ Launching `./tests/modules/gatk4/genotypegvcfs/main.nf` [desperate_engelbart] - revision: 75e2109e4c
   3   │ Creating env using conda: conda-forge::tar=1.32 [cache /home/runner/pytest_workflow_swc64_9s/gatk4_genotypegvcfs_test_gatk4_genotypegvcfs_gendb_input/work/conda/env-c201faffdf42f507ecde3741b6d89378]
   4   │ [8e/2e5f2c] Submitted process > test_gatk4_genotypegvcfs_gendb_input:UNTAR (test_genomicsdb.tar.gz)
   5   │ WARN: Input tuple does not match input set cardinality declared by process `test_gatk4_genotypegvcfs_gendb_input:GATK4_GENOTYPEGVCFS` -- offending value: [[id:test], /home/runner/pytest_workflow_swc64_9s/gatk4_genotypegvcfs_test_gatk4_genotypegvcfs_gendb_input/work/8e/2e5f2c8691120bf42825094839b608/test_genomicsdb, [], []]
   6   │ Execution aborted due to an unexpected error
   7   │ 
   8   │  -- Check script 'tests/modules/gatk4/genotypegvcfs/../../../../modules/gatk4/genotypegvcfs/main.nf' at line: 2 or see '.nextflow.log' file for more details
───────┴──────

Across all three containers it fails, so I'm guessing it's an issue with the module and not the packaging.

edmundmiller avatar Mar 18 '22 13:03 edmundmiller