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12. FAQs
These workflows look for specific file naming patterns, which are defined in the config file. Please be sure that the pattern defined in the config matches to the input file naming convention, and the sample name(s) have been entered in the proper location in the config file. More information about that is available in the Getting Started wiki page.
If the workflows are being run offline, please check to make sure all of the necessary containers, databases, and other files are downloaded to process the input files. This can be done by running the download_offline_files.py script with the associated flags for the workflows that you wish to run. More information about that is available on the Offline Setup wiki page.
Snakemake has trouble processing certain characters, such as dashes "-" in filenames. We recommend that dashes be replaced in filenames with underscores "_" or another character to avoid any problems with snakemake processing the files.
Yes, it is possible to run the metagenomics workflows online! This eliminates the need to download Singularity images and databases prior to execution of the workflows, which means the Offline Setup steps can be skipped. To prepare the workflows for online execution, edits need to be made to the /workflows/config/default_workflowparams.settings file. In every location that specifies biocontainers to "use_local": , change the parameter to False, .
By changing this from True to False, snakemake will download Singularity images during workflow execution rather than working with locally downloaded versions. After these changes are made, the workflows can be run in the same way as they would offline. Please see the wiki documentation pages for more information about how to run each workflow.
This was added in v1.2 to allow snakemake to recognize different input file naming conventions. Specifically, this tag is used to distinguish the Illumina FASTQ samples naming convention (i.e. {sample}_S*_L001_R1.fastq.gz) from inputs with the naming convention of {sample}_1_reads.fq.gz.