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change stageInMode to copy and update module #7014

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change stageInMode to copy and update module #7014

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11b1de2
change copy and update module
famosab Nov 18, 2024
ede08b1
Merge branch 'master' into apply
sateeshperi Nov 19, 2024
ca9e8fd
Merge branch 'master' into apply
SPPearce Nov 19, 2024
a6fb557
Merge branch 'master' into apply
famosab Nov 21, 2024
93cd6e3
fix include statement
mashehu Nov 21, 2024
2990823
revert formatting
famosab Nov 22, 2024
b3e1d5c
Merge branch 'master' into apply
mashehu Nov 25, 2024
b18a597
try to run everything on github runners
mashehu Nov 25, 2024
f9099e4
Revert "try to run everything on github runners"
mashehu Nov 25, 2024
4aa22ff
add gpu tag
mashehu Nov 25, 2024
5cb128a
add back conda exclusion step
mashehu Nov 25, 2024
f1d472c
add path as input to nf-test job
mashehu Nov 25, 2024
1e367ec
try everything on self hosted to better inspect error
mashehu Nov 25, 2024
01cb1e3
try different if clause
mashehu Nov 25, 2024
d164705
run on github runners again
mashehu Nov 25, 2024
f45d5d9
use correct parameter names
mashehu Nov 25, 2024
0f7f69c
fix typo
mashehu Nov 25, 2024
fdc6130
Merge branch 'master' into apply
mashehu Nov 26, 2024
cfd099b
try different skipping condition
mashehu Nov 26, 2024
057459b
add nf-test-changes step back to exclude conda tests
mashehu Nov 26, 2024
928a836
use correct syntax for multiple profiles
mashehu Nov 26, 2024
b47893b
fix input
mashehu Nov 26, 2024
596fa1b
fix exclude setting
mashehu Nov 26, 2024
c7bedce
check only specified tests paths
mashehu Nov 26, 2024
6f1868d
Merge branch 'master' into apply
mashehu Nov 26, 2024
6d933cb
use same logic in nf-test and gpu-test to detect changes
mashehu Nov 28, 2024
fbd0bea
Merge branch 'apply' of github.com:famosab/modules into apply
mashehu Nov 28, 2024
ca7f40a
Merge branch 'master' into apply
mashehu Nov 28, 2024
735eee7
add to conda_skip
famosab Dec 2, 2024
b2356af
use correct exclude statement
mashehu Dec 2, 2024
21b5d83
delete conda_skip list (is part of nf-test.yml again)
mashehu Dec 2, 2024
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2 changes: 2 additions & 0 deletions .github/conda_skip.yml
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Expand Up @@ -182,3 +182,5 @@ exclude:
path: modules/nf-core/xeniumranger/resegment
- profile: conda
path: modules/nf-core/xeniumranger/import-segmentation
- profile: conda
path: modules/nf-core/parabricks/applybqsr
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6 changes: 3 additions & 3 deletions modules/nf-core/parabricks/applybqsr/tests/main.nf.test
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Expand Up @@ -113,7 +113,7 @@ nextflow_process {
input[4] = [
[ id:'reference'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
]
"""
}
}
Expand Down Expand Up @@ -157,7 +157,7 @@ nextflow_process {
input[4] = [
[ id:'reference'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
]
"""
}
}
Expand Down Expand Up @@ -197,7 +197,7 @@ nextflow_process {
input[4] = [
[ id:'reference'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
]
"""
}
}
Expand Down