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add nextflow d30e48d

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Kevin
2026-04-29 23:01:54 +02:00
parent d0b12d668d
commit 97cc9058d3
2840 changed files with 730250 additions and 0 deletions
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32
nextflow/tests-v1/checks/s3-files.nf/.checks Normal file
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set -e
export NXF_PLUGINS_DEFAULT=nf-amazon
# Skip test if AWS keys are missing
if [[ ! $AWS_ACCESS_KEY_ID ]]; then
echo "Skip s3-files test since AWS keys are not available"
exit 0
fi
#
# run normal mode
#
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (gut)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (liver)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > bar (lung)'` == 1 ]] || false
cmp stdout .expected || false
#
# run resume mode
#
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (gut)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (liver)'` == 1 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > bar (lung)'` == 1 ]] || false
cmp stdout .expected || false

10
nextflow/tests-v1/checks/s3-files.nf/.expected Normal file
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>1 dna:chromosome chromosome:Galgal4:1:48849500:49020500:1
TGAAGCTTATCGTGTACTCTGTCTTCAGAAGCACAAGGACAATTAACATTCAATAGCAAG
GTCCTGTATTTATTTGTCTGAATAAATAAATAAGCATAATATATAATAAATAAATACTAT
TCAGCCTCTCACCAATAACAATAGTACCCACGCACATATTGCATAATTACAAAACATCCT
GACAGATCTGTGTGGGTGATAGACCAGAAATACCAGCTCAAATTAACTCTACAAAGAACT
ATATCATGGAACTTAGTGAAAAGTGATTTTTGGTTCCTGATTCTATGGCGCTTTGTTCTG
ACCTCTGTTTCATTGGATAATAAACAACCAGACTAGATTAAACAGTGTGTATTTGAAACA
GAAAATCAGTATAGACTTCCTGATTGAAATCTATTCTCAATCTTCTGGAATGCTCAAAGA
TACTCAGGAATAGAAATTGGAAGAGCAAAAATATCGACAAATTTGTTCCATGAGCTCCCT
CAACCTTTGTAAGATTACTCTCTGTGCAGTAGTTTTCTAGTCCTTTTTCAGTGGTTGATG