Hello, qiime2 users community!
I have the following set-up:
- a huge collection of .fastq files which I would like to process with the dada2 pipeline
- a remote cluster of servers with the separated storage where those files are stored, and the working machines for computing.
Question: Is it possible to import the data from the directory which is not currently used (i.e. from the storage to the working directory)?
It seems that it was not possible before, according to this post from jwdebelius.
The command I use in the $cwd:
qiime demux summarize \ --i-data $storage_dir/test.qza \ --o-visualization test.qzv
The message error:
(1/2) Invalid value for '--i-data': 'q2-import/$storage_dir/test.qza' is not a valid filepath (2/2) Invalid value for '--o-visualization': Directory 'q2-import/$storage_dir' does not exist, cannot save 'test.qzv' into it.
If I run the same command having the data (test.qza) in the
$cwd, everything works just fine.