Running the test problem

[lmszydlowski]

I installed the module and ran into an error while running the "python workflow/short-read-quality-control.py test"

In every case I receive the following error:

Building DAG of jobs... WorkflowError: MissingInputException: Missing input files for rule init_statistics: output: /camp_short-read-quality-control/test_out/short_read_qc/4_summary/uhgg_read_stats.csv wildcards: sample=4_summary/uhgg affected files: /camp_short-read-quality-control/test_out/tmp/4_summary/uhgg_2.fastq.gz /camp_short-read-quality-control/test_out/tmp/4_summary/uhgg_1.fastq.gz MissingInputException: Missing input files for rule init_statistics: output: /camp_short-read-quality-control/test_out/short_read_qc/uhgg_read_stats.csv wildcards: sample=uhgg affected files: /camp_short-read-quality-control/test_out/tmp/uhgg_1.fastq.gz /camp_short-read-quality-control/test_out/tmp/uhgg_2.fastq.gz MissingInputException: Missing input files for rule step_statistics: output: /camp_short-read-quality-control/test_out/short_read_qc/4_summary/uhgg_read_stats.csv wildcards: step=4_summary, sample=uhgg affected files: /camp_short-read-quality-control/test_out/short_read_qc/4_summary/uhgg_2.fastq.gz /camp_short-read-quality-control/test_out/short_read_qc/4_summary/uhgg_1.fastq.gz

In test_out/tmp/ there were uhgg_1.fastq and uhgg_2.fastq files

I instead used "python workflow/short-read-quality-control.py -s configs/samples.csv -r configs/resources.yaml -p configs/parameters.yaml -d test_data/test_out/"

and test dataset was successfully processed.

[lauren-mak]

I've patched this issue in today's update so if you pull it, it should be fixed. Thanks for using it!