Make jobs automatically resubmit for a much wider range of exit codes

[ewels]

now 130..145

Discussion in #configs channel on the nf-core Slack.

'cc @pontus @pcantalupo @muffato @FelixKrueger

'cc @nf-core/core for visibility as this is a fairly wide ranging change (though hopefully not controversial)

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #2170 (6ff70af) into dev (110cec8) will increase coverage by 0.08%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev    #2170      +/-   ##
==========================================
+ Coverage   71.54%   71.62%   +0.08%     
==========================================
  Files          77       77              
  Lines        8367     8375       +8     
==========================================
+ Hits         5986     5999      +13     
+ Misses       2381     2376       -5     

Impacted Files	Coverage Δ
nf_core/bump_version.py	89.47% <ø> (ø)
nf_core/create.py	65.01% <ø> (+0.38%)	⬆️
nf_core/download.py	52.72% <ø> (ø)
nf_core/launch.py	63.26% <ø> (ø)
nf_core/lint/__init__.py	74.18% <ø> (ø)
nf_core/lint/files_unchanged.py	72.61% <ø> (ø)
nf_core/lint/template_strings.py	87.50% <ø> (ø)
nf_core/list.py	79.82% <ø> (ø)
nf_core/modules/bump_versions.py	63.90% <ø> (ø)
nf_core/utils.py	82.38% <ø> (+0.24%)	⬆️
... and 8 more

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[FriederikeHanssen]

sounds reasonable

[muffato]

I noticed that 104 is not in the list anymore. Does anyone remember why it was needed and if it's still relevant ?

@ewels you were in fact involved in 104 getting into the pipeline template ;) #2170, which is a port from nf-core/rnaseq#56

[ewels]

Oof, good spot + detective work @muffato! No I have no memory of why it was there. Presumably saw it somewhere..

Had a quick look in Slack and didn't find a lot, but one or two messages / google suggest that it could crop up as an out-of-memory exit code sometimes. I guess we can add it back here 👍🏻

Anyone got some quick-fire groovy skills to add it into the array in a nice succinct way? Does 104 + 130..145 or something work?

[ewels]

Haven't properly tested the last commit but should hopefully be ok to merge now 👍🏻

[muffato]

A minor change to match the changelog with the code

[ewels]

Black released a new stable update, which is why everything is breaking. Re-ran Black here to fix the tests.