recover: When file inputs are wrong, error is not graceful

[wwood]

I hazily tried to run aviary where I'd not tab completed one of the input files. Took me a bit of time to work out what was going wrong - be good if there was a check in place to make sure input files are real, and not leave it to snakemake:

(poor formatting below, but you get the idea)

(aviary-dev)cl5n006:20241208:~/git/singlem/test/data/appraise_example_with_base_data$ aviary recover -1 SRR5040536_1 -2 SRR5040536_2.fastq.gz -o aviary_out                   12/08/2024 07:02:17 AM INFO: Time - 07:02:17 08-12-2024
12/08/2024 07:02:17 AM INFO: Command - /home/woodcrob/e/aviary-dev/bin/aviary recover -1 SRR5040536_1 -2 SRR5040536_2.fastq.gz -o aviary_out                                  12/08/2024 07:02:17 AM INFO: Version - 0.10.0
12/08/2024 07:02:17 AM WARNING: No assembly provided, assembly will be created using available reads...                                                                       12/08/2024 07:02:17 AM INFO: Configuration file written to /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/aviary_out/config.yaml            12/08/2024 07:02:17 AM INFO: Executing: snakemake --snakefile /mnt/hpccs01/home/woodcrob/git/aviary/aviary/modules/Snakefile --directory /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/aviary_out --cores 16 --rerun-incomplete --keep-going  --rerun-triggers mtime --configfile /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/aviary_out/config.yaml --nolock  --retries 0 --conda-frontend mamba --resources mem_mb=256000   --use-conda --conda-prefix /work/microbiome/conda/_aviary_envs/0.9.2   recover_mags

... (snip)

Assuming unrestricted shared filesystem usage.
host: cl5n006
Building DAG of jobs...
WorkflowError:
MissingInputException: Missing input files for rule qc_short_reads:                                                                                                               output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:                                                                                                                                                                   /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         MissingInputException: Missing input files for rule qc_short_reads:                                                                                                               output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:                                                                                                                                                                   /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         WorkflowError:                                                                                                                                                                    MissingInputException: Missing input files for rule qc_short_reads:
        output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:                                                                                                                                                                   /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         MissingInputException: Missing input files for rule qc_short_reads:
        output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:
            /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         MissingInputException: Missing input files for rule qc_long_reads:
        output: data/long_reads.fastq.gz
        affected files:
            none
    MissingInputException: Missing input files for rule qc_short_reads:
        output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:
            /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         MissingInputException: Missing input files for rule qc_long_reads:                                                                                                                output: data/long_reads.fastq.gz                                                                                                                                              affected files:                                                                                                                                                                   none
WorkflowError:                                                                                                                                                                    MissingInputException: Missing input files for rule qc_short_reads:                                                                                                               output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:                                                                                                                                                                   /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         MissingInputException: Missing input files for rule qc_short_reads:                                                                                                               output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:                                                                                                                                                                   /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         MissingInputException: Missing input files for rule qc_long_reads:                                                                                                                output: data/long_reads.fastq.gz                                                                                                                                              affected files:                                                                                                                                                                   none                                                                                                                                                                  MissingInputException: Missing input files for rule qc_short_reads:                                                                                                               output: data/short_unmapped_ref.bam, data/short_reads.fastq.gz, data/short_filter.done                                                                                        affected files:                                                                                                                                                                   /mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/SRR5040536_1                                                                         MissingInputException: Missing input files for rule qc_long_reads:                                                                                                                output: data/long_reads.fastq.gz                                                                                                                                              affected files:                                                                                                                                                                   none                                                                                                                                                              12/08/2024 07:02:18 AM 
CRITICAL: Command '['snakemake', '--snakefile', '/mnt/hpccs01/home/woodcrob/git/aviary/aviary/modules/Snakefile', '--directory', '/mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/aviary_out', '--cores', '16', '--rerun-incomplete', '--keep-going', '--rerun-triggers', 'mtime', '--configfile', '/mnt/hpccs01/home/woodcrob/git/singlem/test/data/appraise_example_with_base_data/aviary_out/config.yaml', '--nolock', '--retries', '0', '--conda-frontend', 'mamba', '--resources', 'mem_mb=256000', '--use-conda', '--conda-prefix', '/work/microbiome/conda/_aviary_envs/0.9.2', 'recover_mags']' returned non-zero exit status 1.