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Unquoted values in params section of a config file -- eg false -- get quoted as strings in seqera platform params #418

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cmatKhan opened this issue Jun 7, 2024 · 0 comments

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@cmatKhan
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cmatKhan commented 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:

    dbsnp = false
    dbsnp_tbi = false
    known_indels = false
    known_indels_tbi = false
    known_snps = false
    known_snps_tbi = false
    known_indels_vqsr = false
    known_snps_vqsr = false
    ngscheckmate_bed = false

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:

"dbsnp":"false","dbsnp_tbi":"false","dbsnp_vqsr":"false"

Removing the quotes from the boolean values and re-launching fixed the problem -- the pipeline succeeded

@cmatKhan 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
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