Genomad directory naming error

[mflynn-lanl]

Workflow Name
Viruses and Plasmids

Project URL
https://nmdc-edge.org/admin/project?code=G6y3fesWmFRVN7X5

Additional Info
stderr:
mv: cannot stat '/expanse/projects/nmdc/edge_app/nmdc-edge/io/projects/lFOIv57dUD9b5nBd/output/virus_plasmid/mvJw6v7nKqAFB_summary/': No such file or directory
The directory should be named:
/expanse/projects/nmdc/edge_app/nmdc-edge/io/projects/lFOIv57dUD9b5nBd/output/virus_plasmid/mvJw6v7ngfaKqAFB_summary/

for some reason fa is deleted from directory name

[mflynn-lanl]

This is still an issue:
Emiley forwarded me an email from a user with a failed genomad project. It looks like the problem was with how the output directory name was generated. It's supposed to use the fasta file name (AF020713.1_summary) but the summary directory is actually named 16752349578611082575_summary (the name in the call-gn/inputs directory) which is why we get the error
mv: cannot stat '/expanse/projects/nmdc/edge_app/nmdc-edge/io/projects/Pjes7aJqzCOV6Rnu/output/virus_plasmid/AF020713.1_summary/': No such file or directory
Looks like the problem is it's using the wrong file name for ASM_FASTA
String prefix=sub(sub(sub(sub(sub(sub(basename(ASM_FASTA), "\.fna", ""), "\.fasta", ""), "\.fa", ""), "\.fna\.gz", ""), "\.fasta\.gz", ""), "\.fa\.gz", "")
Can we change it so that it moves whatever directory is in the Cromwell execution directory *_summary to the project output directory? Right now it uses mv {OUTDIR}/{prefix}_summary/ ~{GeNomad_Summary} to move the files. How should I change it to use *_summary ? Also, it's not moving the files to GeNomad_Summary (OUTDIR + '/geNomad_summary')

[chienchi]

One workaround I think it will work:

1. Probably add project name as an input in the template(input tmpl and wdl tmpl) and also the wdl files
2. use the project name as prefix for the output directory prefix instead of rely on input file which could be dynamic renamed when it is from URL.
3. copy or symlink the ~{ASM_FASTA} to ~{projname} and use ~{projname} as input for genomad. (replace ~{ASM_FASTA} to ~{projname} in command section of task geNomad_full)