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Unknown config attribute with test_tsv profile with Nextflow 20.04 #631

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maxibor opened this issue Dec 10, 2020 · 3 comments · Fixed by #663
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Unknown config attribute with test_tsv profile with Nextflow 20.04 #631

maxibor opened this issue Dec 10, 2020 · 3 comments · Fixed by #663
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@maxibor
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maxibor commented Dec 10, 2020

Description of the bug

Running the dev branch of eager, (as of commit b916b6d) with the test_tsv profile and Nextflow version 20.04.1 leads to this error:

$ nextflow run main.nf -profile test_tsv,singularity --single_end
N E X T F L O W  ~  version 20.04.1
Launching `main.nf` [nasty_coulomb] - revision: 0cb20d25f3
Unknown config attribute `params.genomes.GRCh37.projectDir` -- check config file: /projects1/users/borry/23_eager/test/eager/nextflow.config

Running it NF 20.10 fixes the issue.

Steps to reproduce

Steps to reproduce the behaviour:

$ nextflow run main.nf -profile test_tsv,singularity --single_end
  • Hardware: Slurm HPC, and Mac

Nextflow Installation

  • Version: 20.04.1 -->

Container engine

  • Singularity and Docker
@maxibor maxibor added the bug Something isn't working label Dec 10, 2020
@jfy133 jfy133 added the needs upstream fix Needs a fix in the upstream tool project label Dec 10, 2020
@jfy133
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jfy133 commented Dec 10, 2020

$ export NXF_VER=20.04.0
$ nextflow run main.nf -profile test_tsv,singularity --single_end
N E X T F L O W  ~  version 20.04.0
Launching `main.nf` [reverent_feynman] - revision: fe08e6a5fa
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/eager v2.2.3dev
----------------------------------------------------
$ export NXF_VER=20.04.1
$ nextflow run main.nf -profile test_tsv,singularity --single_end
N E X T F L O W  ~  version 20.04.1
Launching `main.nf` [clever_banach] - revision: fe08e6a5fa
Unknown config attribute `params.genomes.GRCh37.projectDir` -- check config file: /home/jfellows/Documents/git/maxibor/eager/nextflow.config
$ export NXF_VER=20.05.0-edge
$ nextflow run main.nf -profile test_tsv,singularity --single_end
N E X T F L O W  ~  version 20.05.0-edge
Launching `main.nf` [fabulous_booth] - revision: fe08e6a5fa
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/eager v2.2.3dev
----------------------------------------------------

This was a specific bug in Nextflow 20.04.1, which was then fixed in the next release. This is an edge case so we can close for now

@jfy133 jfy133 closed this as completed Dec 10, 2020
@jfy133 jfy133 reopened this Jan 14, 2021
@jfy133
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jfy133 commented Jan 14, 2021

We need to bump the minimum Nextflow version for eager unfortunately. By default e.g. aws will take the latest patch release of a version, so even though 20.04.0 does work, AWS will pull 20.04.1 and will crash :\

@jfy133 jfy133 self-assigned this Jan 14, 2021
@jfy133 jfy133 removed the needs upstream fix Needs a fix in the upstream tool project label Jan 14, 2021
@jfy133 jfy133 mentioned this issue Jan 14, 2021
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@apeltzer
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Fixed by #663

phue added a commit to phue/methylseq that referenced this issue Mar 24, 2021
this is mainly to prevent breakage with aws. x-ref nf-core/eager#631
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