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