Altocumulus tries to upload BCL folders or FASTQ files before checking if the provided path is a Cloud URI or a local path. It brings problems, because Python's os.path.abspath("gs://bucket-name/folder-name") returns the following string:
/path/to/local/cwd/gs://bucket-name/folder-name
and thus the sample sheet uploading fails.
Solution
I reorganize the checking on path at the BCL/FASTQ step to include the checking on if it is a Cloud URI (only consider S3 and GS URIs for now). And if encountering a Cloud URI, simply skip the rest of process and go to the next path.
Issue
Altocumulus tries to upload BCL folders or FASTQ files before checking if the provided path is a Cloud URI or a local path. It brings problems, because Python's
os.path.abspath("gs://bucket-name/folder-name")returns the following string:and thus the sample sheet uploading fails.
Solution
I reorganize the checking on
pathat the BCL/FASTQ step to include the checking on if it is a Cloud URI (only consider S3 and GS URIs for now). And if encountering a Cloud URI, simply skip the rest of process and go to the next path.