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However, when I set up the workflow through seqera platform and added this profile, I was getting the following error:
Error executing process > 'NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS (1)'
Caused by:
Can't stage file file:///false -- file does not exist
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run
In the params displayed through the platform interface, the false value was not quoted, but when I looked in the params in the "re-launch" page, I noticed that they were quoted:
Removing the quotes from the boolean values and re-launching fixed the problem -- the pipeline succeeded
The text was updated successfully, but these errors were encountered:
cmatKhan
changed the title
Unquoted strings in a params file -- eg false -- get quoted as strings in seqera platform params
Unquoted values in params section of a config file -- eg false -- get quoted as strings in seqera platform params
Jun 7, 2024
I am working on a slightly modified verion of sarek, and added this config:
https://github.com/cmatKhan/sarek/blob/igvreport/conf/kn99_genotype_check_filter.config
which has the following params:
However, when I set up the workflow through seqera platform and added this profile, I was getting the following error:
In the params displayed through the platform interface, the
false
value was not quoted, but when I looked in the params in the "re-launch" page, I noticed that they were quoted:Removing the quotes from the boolean values and re-launching fixed the problem -- the pipeline succeeded
The text was updated successfully, but these errors were encountered: