79 lines
2.7 KiB
Plaintext
79 lines
2.7 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 --save_bam_bai | tee stdout
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[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
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[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
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[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
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[[ -f results/log/alpha.fastqc.log ]] || false
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[[ -f results/log/beta.fastqc.log ]] || false
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[[ -f results/log/delta.fastqc.log ]] || false
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[[ -f results/align/alpha.bai ]] || false
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[[ -f results/align/alpha.bam ]] || false
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[[ -f results/align/beta.bai ]] || false
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[[ -f results/align/beta.bam ]] || false
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[[ -f results/align/delta.bai ]] || false
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[[ -f results/align/delta.bam ]] || false
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[[ -L results/quant/alpha ]] || false
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[[ -L results/quant/beta ]] || false
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[[ -L results/quant/delta ]] || false
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[[ -f results/samples.csv ]] || false
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[[ -f results/summary.txt ]] || false
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#
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# one more time to make sure 'overwrite' is fine
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#
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echo Second run
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$NXF_RUN --save_bam_bai | tee stdout
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[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
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[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
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[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
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[[ -f results/log/alpha.fastqc.log ]] || false
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[[ -f results/log/beta.fastqc.log ]] || false
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[[ -f results/log/delta.fastqc.log ]] || false
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[[ -f results/align/alpha.bai ]] || false
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[[ -f results/align/alpha.bam ]] || false
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[[ -f results/align/beta.bai ]] || false
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[[ -f results/align/beta.bam ]] || false
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[[ -f results/align/delta.bai ]] || false
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[[ -f results/align/delta.bam ]] || false
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[[ -L results/quant/alpha ]] || false
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[[ -L results/quant/beta ]] || false
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[[ -L results/quant/delta ]] || false
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[[ -f results/samples.csv ]] || false
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[[ -f results/summary.txt ]] || false
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#
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# clean & run resume mode
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#
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echo Third run
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rm -rf results
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$NXF_RUN --save_bam_bai -resume | tee stdout
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[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
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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 > quant') == 3 ]] || false
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[[ -f results/log/alpha.fastqc.log ]] || false
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[[ -f results/log/beta.fastqc.log ]] || false
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[[ -f results/log/delta.fastqc.log ]] || false
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[[ -f results/align/alpha.bai ]] || false
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[[ -f results/align/alpha.bam ]] || false
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[[ -f results/align/beta.bai ]] || false
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[[ -f results/align/beta.bam ]] || false
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[[ -f results/align/delta.bai ]] || false
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[[ -f results/align/delta.bam ]] || false
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[[ -L results/quant/alpha ]] || false
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[[ -L results/quant/beta ]] || false
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[[ -L results/quant/delta ]] || false
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[[ -f results/samples.csv ]] || false
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[[ -f results/summary.txt ]] || false
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