Add early abort and notification when a job-step yields zero files.

[charles-cowart]

A recent job ended in the following error:

Error executing Sequence Processing Pipeline:
['Traceback (most recent call last):\n', ' File "/home/qiita/miniconda3/envs/qp-knight-lab-processing-2022.03/lib/python3.9/site-packages/qiita_client/plugin.py", line 265, in call\n success, artifacts_info, error_msg = task(\n', ' File "/home/qiita/miniconda3/envs/qp-knight-lab-processing-2022.03/lib/python3.9/site-packages/qiita_client/plugin.py", line 105, in call\n return self.function(qclient, server_url, job_id, output_dir)\n', ' File "/home/qiita/qiita_spots/qp-knight-lab-processing/qp_klp/klp.py", line 360, in sequence_processing_pipeline\n fastqc_job = FastQCJob(pipeline.run_dir,\n', ' File "/home/qiita/qiita_spots/mg-scripts/sequence_processing_pipeline/FastQCJob.py", line 41, in init\n self.commands, self.project_names = self._get_commands()\n', ' File "/home/qiita/qiita_spots/mg-scripts/sequence_processing_pipeline/FastQCJob.py", line 65, in _get_commands\n params, additional_project_names = self._scan_fastq_files(False)\n', ' File "/home/qiita/qiita_spots/mg-scripts/sequence_processing_pipeline/FastQCJob.py", line 136, in _scan_fastq_files\n projects = self._find_projects(find_path, is_raw_input)\n', ' File "/home/qiita/qiita_spots/mg-scripts/sequence_processing_pipeline/FastQCJob.py", line 116, in _find_projects\n raise ValueError("indeterminate type")\n', 'ValueError: indeterminate type\n']

This error wasn't the right error to return. As there were zero non-zero files generated, there were no files found with trimmed or filtered in them. The workflow assumes a different situation and returns indeterminate type:

We got to https://github.com/biocore/mg-scripts/blob/32d7a94513c17c2da81761f7100bea13c01ac8ff/sequence_processing_pipeline/FastQCJob.py#L116

We need to early abort when zero usable files are found.