This document describes some issues that may arise in the course of using the workflows, and steps to take to diagnose and correct these issues.

'--fasta': \"${params.fasta}\" is not valid, specify path to reference FASTA"

Nearly all of the reference files necessary to run these pipelines are bundled in the relevant containers. The exception to this is the reference FASTA file, as well as associated indices for the alignment programs. Only the FASTA file is required, the workflows will generate the necessary indices if they are missing. These workflows were developed to work with the naming conventions found in the Ensembl project.

'--sampleID': \"${params.sampleID}\" is not valid, specify a name for this sample"

The workflows require the specification of a sample ID, which is used for naming output files.

'--pbmode': \"${params.pbmode}\" is not valid, supported options are 'CCS' or 'CLR'"

The PacBio aligner requires specification of whether the input data are CCS or CLR, and so this is a required parameter for the pacbio workflow.

Error code: 140 for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.mem} being exceeded. Attempting orderly shutdown. See .command.log in: ${task.workDir} for more info."

We have benchmarked the workflows for a range of inputs, but it is possible that some inputs that are very large or extremely heterogeneous may exceed the default resource allocations we have set. In this case, the module resource allocations would need to be increased.