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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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73
nextflow/tests/checks/publish-dir.nf/.checks Normal file
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#
# run normal mode
#
echo First run
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > my_combine'` == 1 ]] || false
cmp stdout .expected || false
[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false
#
# one more time to make sure 'overwrite' is fine
#
echo Second run
$NXF_RUN | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Submitted process > my_combine'` == 1 ]] || false
cmp stdout .expected || false
[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false
#
# clean & run resume mode
#
echo Third run
rm -rf data
rm -rf more/data
$NXF_RUN -resume | tee stdout
[[ `grep INFO .nextflow.log | grep -c 'Cached process > align'` == 3 ]] || false
[[ `grep INFO .nextflow.log | grep -c 'Cached process > my_combine'` == 1 ]] || false
cmp stdout .expected || false
[[ -f data/alpha.bai ]] || false
[[ -f data/alpha.bam ]] || false
[[ -f data/beta.bai ]] || false
[[ -f data/beta.bam ]] || false
[[ -f data/delta.bai ]] || false
[[ -f data/delta.bam ]] || false
[[ -L data/result.txt ]] || false
[[ -f more/data/result.txt ]] || false
#
# NOTE: on Mac when deleting an hard-link also the origin is removed
#
[[ -f data/xxx/A ]] || false
[[ -f data/xxx/B ]] || false
[[ -f data/xxx/C ]] || false