Chase Mateusiak

This happens to me if I run out of RAM. Not sure if that is the issue, so if it is not, ignore what is below. It looks like you...

I am also unsure why it says there is more than one entry. When I look manually, there is only one entry per organism: ``` > x = map(post_wgd_yeasts, is.genome.available,...

for what it is worth, this did work: ``` avail = map(post_wgd_yeasts, is.genome.available, db="refseq", details=TRUE) test = function(ftp_row){ accession = ftp_row[['assembly_accession']] asm_name = ftp_row[['asm_name']] ftp_addr = ftp_row[['ftp_path']] gtf_filename = paste(accession,...

OK -- I think I have a solution to this. Here is my environment: ``` > sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS Matrix...

hm. that does work. But if I try to download the annotation files and genomes to the same directory, then there is a problem with the attempt to unzip: this...

I am having the same issue. I guess the SGD gene ids are 'ORF' in `org.Sc.sgd.db` -- that should be verified by someone who knows better -- in any case,...

Apologies if this isn't helpful, but you might try using the nf-core modules to pull the already written bwamem2 index and mem modules: https://github.com/nf-core/modules Here is the workflow I use...

Ah -- fantastic. I figured there must be some way of doing this within the framework already. Couldn't figure it out though. Thank you!

OK -- my bad. I didn't update the `test.yml`. It is updated now...I think it will pass?

ugh -- of course. I had this in a config outside of the test module: ``` withName: 'PICARD_ADDORREPLACEREADGROUPS'{ ext.args = {[ "-LB ${meta.id}", "-PL ILLUMINA", "-PU bc1", "-SM ${meta.id}" ].join('...