Within the documentation for running theta_est, there are misleading file names that coupled with a degree of vagueness might confuse users.
nextflow run theta_est.nf --bam toy_dataset/paired_end.bam --fa toy_dataset/paired_end.fa
From the name alone, the FASTA file toy_dataset/paired_end.fa (or the single-ended equivalent) can be mistaken for a readset. I would encourage using names which don't have an irrelevant context, such as "reference.fa".
Within the documentation for running theta_est, there are misleading file names that coupled with a degree of vagueness might confuse users.
From the name alone, the FASTA file
toy_dataset/paired_end.fa(or the single-ended equivalent) can be mistaken for a readset. I would encourage using names which don't have an irrelevant context, such as "reference.fa".Perhaps I am confused here?