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Incompatibility with recent Nextflow version #39

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Cecilia-Sensalari opened this issue May 9, 2022 · 4 comments · Fixed by #43 · May be fixed by #51
Closed

Incompatibility with recent Nextflow version #39

Cecilia-Sensalari opened this issue May 9, 2022 · 4 comments · Fixed by #43 · May be fixed by #51

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@Cecilia-Sensalari
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As pointed out in issue #38, the Nextflow pipeline implemented in main.nf is not compatible anymore with recent Nextflow versions (the issue refers to version 22.04.0.5697). It gives the following error message:

$ nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt
N E X T F L O W  ~  version 22.04.0
Launching `https://github.com/VIB-PSB/ksrates` [determined_bernard] DSL2 - revision: bfbb623720 [master]


K S R A T E S   -   N E X T F L O W   P I P E L I N E   (v1.1.1)
----------------------------------------------------------------

Configuration file:                    ./config_elaeis.txt
Logs folder:                           logs_3cf4463c
Preserve leftover files:               false

Command line:               nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt
Launch directory:           /Users/wickell/ksrates
Work directory:             /Users/wickell/ksrates/work
ksrates directory:          /Users/wickell/.nextflow/assets/VIB-PSB/ksrates

Start time:                 2022-04-28T09:05:59.358787-04:00


No such variable: outCheckConfig

 -- Check script '/Users/wickell/.nextflow/assets/VIB-PSB/ksrates/main.nf' at line: 252 or see '.nextflow.log' file for more details

A quick way to fix this problem is to make use of the older Nextflow version used to develop ksrates (21.10.6.5660) by adding the NXF_VER environmental variable in the command line (see Nextflow docs):

 NXF_VER=21.10.6 nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt

The actual fix will have to identify the cause of this incompatibility and edit the affected lines in main.nf.
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@Cecilia-Sensalari Cecilia-Sensalari linked a pull request Jul 13, 2022 that will close this issue
Add support for Nextflow version 22.03.0-edge and later #43
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@Cecilia-Sensalari Cecilia-Sensalari mentioned this issue Jul 13, 2022
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@Cecilia-Sensalari Cecilia-Sensalari linked a pull request Jun 29, 2023 that will close this issue
Supporting new Nextflow DSL2 syntax #51
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