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dahak-metagenomics / dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
https://dahak-metagenomics.github.io/dahak
BSD 3-Clause "New" or "Revised" License
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Running non-shakya datasets through read filtering: Workflow Error #122

Open nalbright opened 6 years ago

nalbright commented 6 years ago

Executed the following (my new datafiles were specified in sturner_readfilt_workflow_001x.json):

snakemake -p -n --use-singularity --local-cores 4 --configfile=config/sturner_readfilt_workflow_001x.json read_filtering_pretrim_workflow read_filtering_posttrim_workflow

Error received:

WorkflowError in line 405 of /home/nalbright/dahak_2018/dahak/workflows/read_filtering/Snakefile: Duplicate output file pattern in rule quality_trimming. First two duplicate for entries 0 and 1 File "/home/nalbright/dahak_2018/dahak/workflows/Snakefile", line 14, in File "/home/nalbright/dahak_2018/dahak/workflows/read_filtering/Snakefile", line 405, in

Any ideas what I am doing wrong?

charlesreid1 commented 6 years ago

The input reads file pattern that is used to do read filtering has (probably )changed, so the Snakemake configuration file should account for that. You can update the following parameter in your configuration (shown here with default values, not sure how direction is specified):

    "read_filtering" : {
        "read_patterns" : {
            "pre_trimming_pattern"  : "{sample}_{direction}_reads.fq.gz",
            "post_trimming_pattern" : "{sample}_{direction}.trim{qual}.fq.gz",
        }
    }

(also note, if the files are present in your data/ directory, the URL for each read file is never actually used, so you can just set it to an empty string)