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442f3e3
Force dedup memory amount
jfy133 Jun 25, 2020
294626e
Add dedup exit code 1 for retry when heapspace issue and add empty ce…
jfy133 Jun 30, 2020
a281d22
Merge pull request #49 from nf-core/dev
jfy133 Jun 30, 2020
088d0c7
Fix emailing with mailutils to actually include body
jfy133 Jun 30, 2020
808446b
Sync emailing system to nf-core/tools
jfy133 Jun 30, 2020
5982ddf
Merge pull request #50 from nf-core/dedup-gc-overhead-fix
jfy133 Jun 30, 2020
d36a896
Fix command
jfy133 Jun 30, 2020
7bca81c
Merge pull request #51 from nf-core/dedup-gc-overhead-fix
jfy133 Jun 30, 2020
f04bf3c
Adding extra validation of input after bug reports
jfy133 Jul 8, 2020
0c154fd
Revert param validation check as mis-typed suggestion is nextflow inv…
jfy133 Jul 8, 2020
470ea41
Merge branch 'dev' into let-me-commit
jfy133 Jul 8, 2020
e8273d4
Merge pull request #493 from jfy133/let-me-commit
jfy133 Jul 8, 2020
8b77a0a
Remove leftover unused MaltExtract parameter
jfy133 Jul 8, 2020
6317149
Create remove
ZandraFagernas Jul 12, 2020
509c8b4
Add files via upload
ZandraFagernas Jul 12, 2020
717d7ab
Delete remove
ZandraFagernas Jul 12, 2020
7925130
Create remove
ZandraFagernas Jul 12, 2020
2dce470
Add files via upload
ZandraFagernas Jul 12, 2020
e61b4fc
Delete remove
ZandraFagernas Jul 12, 2020
6657beb
Create remove
ZandraFagernas Jul 12, 2020
7cd19a0
Add files via upload
ZandraFagernas Jul 12, 2020
4160aea
Delete remove
ZandraFagernas Jul 12, 2020
29984bd
Create remove
ZandraFagernas Jul 12, 2020
1ce093b
Add files via upload
ZandraFagernas Jul 12, 2020
ecb7c81
Delete remove
ZandraFagernas Jul 12, 2020
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5 changes: 5 additions & 0 deletions conf/base.config
Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,11 @@ process {
errorStrategy = { task.exitStatus in [141] ? 'ignore' : 'retry' }
}

// Add 1 retry for certain java tools as not enough heap space java errors gives exit code 1
withName: dedup {
errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' }
}

// Add 1 retry as not enough heapspace java error gives exit code 1
withName: malt {
errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' }
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