ERROR ~ Unknown method invocation getBaseName on String type
#530
Comments
|
Just encountered the same issue : def busco_db = file(params.busco_db)
if (busco_db.getBaseName().contains('odb10')) {Also ping @jfy133 |
|
There's also a similar issue in if ( !ch_centrifuge_db_file.isEmpty() ) {
if ( ch_centrifuge_db_file.extension in ['gz', 'tgz'] ) {
// Expects to be tar.gz!
ch_db_for_centrifuge = CENTRIFUGE_DB_PREPARATION ( ch_centrifuge_db_file ).db
} else if ( ch_centrifuge_db_file.isDirectory() ) {
ch_db_for_centrifuge = Channel
.fromPath( "${ch_centrifuge_db_file}/*.cf" )
} else {
ch_db_for_centrifuge = Channel.empty()
}
} else {
ch_db_for_centrifuge = Channel.empty()
}
// Centrifuge val(db_name) has to be the basename of any of the
// index files up to but not including the final .1.cf
ch_db_for_centrifuge = ch_db_for_centrifuge
.collect()
.map{
db ->
def db_name = db[0].getBaseName().split('\\.')[0]
[ db_name, db ]
}The map needs to be moved inside the |
|
In the upcoming patch release :) |
|
Hi! I have the same issue and, although I see that you are planning to fix this in the next release, I wonder how I could fix it without updating the pipeline? Once I tried to update it and resume and it started the entire process from the very beginning, so I would like to avoid that this time (especially since I'm very close to finish with the processing after so many months). |
|
Hi @mtva0001 the fix is already out in 2.5.3. However it's very hard to say whether it will start from the beginning again or not :/. The only thing I can recommend is to try and copy the 'fix' that is in 2.5.3 into your local copy of the pipeline, and then try to resume from there. The fix in particular is: https://github.com/nf-core/mag/blob/master/subworkflows%2Flocal%2Fgtdbtk.nf#L28-L29
However I can't guarantee this will work though... Sorry. The resuming thing is a little mysterious |
|
Thanks a lot! It seems it worked! :) |
Description of the bug
hi I have been running Mag Pipeline for some days, and I ran into this error: see below
What can we do to fix this?
Command used and terminal output
Relevant files
configuration and log file.zip
System information
N E X T F L O W ~ version 23.04.1
HPC
Singularity
Ubuntu
Version of nf-core/mag 2.5
The text was updated successfully, but these errors were encountered: