Hi Ollie, we had an issue where a gene (actually an intron) was annotated in just one sample. For obvious reasons it wasn't possible to create an alignment or use IQtree, but it would be nice if the pipeline didn't stop with an error (rules: alignment-trim, iqtree and plot-tree). To that end, we modified the snakefile (in case of less than two occurences, input is copied to output, which prevents Snakemake job execution failure), but not on your latest version. I think the changes can be merged, but have not tested it.
Hi Ollie, we had an issue where a gene (actually an intron) was annotated in just one sample. For obvious reasons it wasn't possible to create an alignment or use IQtree, but it would be nice if the pipeline didn't stop with an error (rules: alignment-trim, iqtree and plot-tree). To that end, we modified the snakefile (in case of less than two occurences, input is copied to output, which prevents Snakemake job execution failure), but not on your latest version. I think the changes can be merged, but have not tested it.
As for commit 204d201; shouldn't -g5=h be -b5=h ?