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Updated Sanger config for the new LSF queues#1130

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jfy133 merged 1 commit into
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sanger_queues
Jun 16, 2026
Merged

Updated Sanger config for the new LSF queues#1130
jfy133 merged 1 commit into
masterfrom
sanger_queues

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@muffato

@muffato muffato commented Jun 12, 2026

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The LSF queues at the Sanger are changing. The farm22 and tol22 now have different queue configurations, so I've moved the queue settings to the farm-specific files.

@muffato muffato self-assigned this Jun 12, 2026
@muffato

muffato commented Jun 12, 2026

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Why is the CI testing all config files ?

@muffato

muffato commented Jun 12, 2026

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I don't know what https://github.com/nf-core/configs/actions/runs/27430916781/job/81080792432?pr=1130 means

/home/runner/work/configs/configs/conf/sanger.config:32:9: `clustername` was assigned but not declared
 32 |     def clustername = "farm22"
    |         ^^^^^^^^^^^

/home/runner/work/configs/configs/conf/sanger.config:35:9: `clustername` was assigned but not declared
 35 |         clustername = ['/bin/bash', '-c', 'lsid | awk \'$0 ~ /^My clus
    |         ^^^^^^^^^^^

/home/runner/work/configs/configs/conf/sanger.config:37:103: `clustername` is not defined
 37 | ot run lsid to determine current cluster, defaulting to "+clustername)
    |                                                           ^^^^^^^^^^^

/home/runner/work/configs/configs/conf/sanger.config:40:9: `clustername` is not defined
 40 |     if (clustername == "tol22") {
    |         ^^^^^^^^^^^

/home/runner/work/configs/configs/conf/sanger.config:42:16: `clustername` is not defined
 42 |     } else if (clustername == "farm22") {
    |                ^^^^^^^^^^^

Is def clustername not declaring the variable ?

@pontus

pontus commented Jun 15, 2026

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What you're seeing is unfortunate fallout from the process to move to the new, stricter config parser. Things not referring to your profile can be ignored.

@pontus

pontus commented Jun 15, 2026

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Normally we expect the PR submitter to merge when suitable after approval, but due to the current work to move to strict syntax, it may not be possible, let us know if you need assistance to merge.

@jfy133

jfy133 commented Jun 16, 2026

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Will merge on your behalf ;)

@jfy133 jfy133 merged commit 6cb8298 into master Jun 16, 2026
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@jfy133 jfy133 deleted the sanger_queues branch June 16, 2026 07:48
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4 participants