Export Reads fails when there are unprocessed FASTQs on disk

[jameshadfield]

To reproduce:

Run the current master (version 1.1.0[rc*]) from source using the provided EBOV example data

cd example_data/20181008_1405_EBOV
rampart --protocol ../../example_protocols/EBOV/ --verbose --clearAnnotated

While the data is still being processed by RAMPART -- i.e. there are more FASTQs on disk than have been demuxed, mapped & ingested by RAMPART, trigger the "Export Reads" pipeline for a sample (e.g. "Kikwit"). You'll get the following error:

snakemake --snakefile /Users/naboo/github/artic-network/rampart/default_protocol/pipelines/bin_to_fastq/Snakefile --configfile /Users/naboo/github/artic-network/rampart/default_protocol/pipelines/bin_to_fastq/config.yaml --config sample_name=Kikwit barcodes=NB03 samples="{Kikwit: [NB03]}" annotated_path=/Users/naboo/github/artic-network/rampart/example_data/20181008_1405_EBOV/annotations/ basecalled_path=/Users/naboo/github/artic-network/rampart/example_data/20181008_1405_EBOV/fastq/pass/ output_path=/Users/naboo/github/artic-network/rampart/example_data/20181008_1405_EBOV --nolock --rerun-incomplete
...
  File "/Users/naboo/miniconda3/envs/artic-rampart/bin/binlorry", line 8, in <module>
    sys.exit(main())
  File "/Users/naboo/miniconda3/envs/artic-rampart/lib/python3.7/site-packages/binlorry/binlorry.py", line 69, in main
    args.verbosity, args.print_dest, args.out_report)
  File "/Users/naboo/miniconda3/envs/artic-rampart/lib/python3.7/site-packages/binlorry/binlorry.py", line 157, in process_files
    report_file = report_dict[read_file]
KeyError: '/Users/naboo/github/artic-network/rampart/example_data/20181008_1405_EBOV/fastq/pass/fastq_runid_e9e588bddbea1984a1556c61a8d53decbecf82e2_1.fastq'

After all FASTQs have been processed and are displayed in RAMPART, you can trigger the pipeline for the same sample without any issues. The snakemake call is identical.