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[Internal] [Bug] Nextflow version 24.04.2 and nextflow.config tower configuration incompatibility #210

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jessicarowell opened this issue Nov 7, 2024 · 1 comment
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@jessicarowell
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The tower param specification in nextflow.config seems to be incompatible with Nextflow version 24.04.2.

It works in 24.04.3 and 24.04.4.

Place an ❌ in a Box that Best Matches the Bug's Importance:

  • [] 1 - Most severe (a full-break in core function)
  • 2-4 - Moderate (break for a particular aspect/feature) (how integral is the broken feature?)
  • [] 5 - Least severe (non-functional issue, such as inconsitency / error in documentation or administrative in nature) 

Please Complete the Following Information:

  • OS: [e.g. iOS]: CDC on-prem
  • Browser [e.g. chrome, safari]: N/A
  • Version [e.g. 22]: Nextflow 24.04.2
  • Run environment (container, cloud service, HPC, platform, etc.): on-prem, not HPC

nextflow run main.nf -profile test,singularity --species virus --submission --sra --biosample --output_dir test --submission_config ~/02.scratch/submission_config.yaml

Nextflow 24.10.0 is available - Please consider updating your version to it

N E X T F L O W ~ version 24.04.2

Launching main.nf [marvelous_waddington] DSL2 - revision: 92b49e04b8

[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:VALIDATE_PARAMS -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:METADATA_VALIDATION -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:REPEATMASKER -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:LIFTOFF_CLI -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:CONCAT_GFFS -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:GET_WAIT_TIME -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:SUBMISSION -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:WAIT -
[- ] process > TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:UPDATE_SUBMISSION -
ERROR ~ Error executing process > 'TOSTADAS_WORKFLOW:TOSTADAS:VALIDATE_PARAMS'

Caused by:
For input string: ""

-- Check '.nextflow.log' file for details

@jessicarowell jessicarowell added the bug Something isn't working label Nov 7, 2024
@jessicarowell jessicarowell self-assigned this Nov 7, 2024
@jessicarowell
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Removed the tower config params

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