81 lines
2.3 KiB
Bash
81 lines
2.3 KiB
Bash
set -e
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get_abs_filename() {
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echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
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}
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export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
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[[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
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set -x
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$NXF_CMD -C ./google.config -q run ./test-arrays.nf > array_output
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[[ `grep 'Hi from the nf-test-array bucket!' -c array_output` == 3 ]] && echo OK || { echo 'Failed array tasks' && false; }
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$NXF_CMD -C ./google.config \
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run ./test-readspair.nf \
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-with-report \
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-with-trace $OPTS
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## complex paths test
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$NXF_CMD -C ./google.config run ./test-complexpaths.nf
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# validate
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[[ -d foo ]] || false
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[[ -e 'foo/.alpha' ]] || false
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[[ -e 'foo/01_A(R1).fastq' ]] || false
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[[ -e 'foo/01_A(R2).fastq' ]] || false
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[[ -e 'foo/f1.fa' ]] || false
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[[ -e 'foo/f2.fa' ]] || false
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[[ -e 'foo/f3.fa' ]] || false
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[[ -e 'foo/hello.txt' ]] || false
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[[ -e 'foo/sample.html' ]] || false
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[[ -e 'foo/sample.zip' ]] || false
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[[ -e 'foo/sample_(1 2).vcf' ]] || false
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rm -rf foo
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$NXF_CMD -C ./google.config run ./test-complexpaths.nf -resume
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[[ -d foo ]] || false
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[[ -e 'foo/.alpha' ]] || false
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[[ -e 'foo/01_A(R1).fastq' ]] || false
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[[ -e 'foo/01_A(R2).fastq' ]] || false
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[[ -e 'foo/f1.fa' ]] || false
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[[ -e 'foo/f2.fa' ]] || false
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[[ -e 'foo/f3.fa' ]] || false
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[[ -e 'foo/hello.txt' ]] || false
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[[ -e 'foo/sample.html' ]] || false
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[[ -e 'foo/sample.zip' ]] || false
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[[ -e 'foo/sample_(1 2).vcf' ]] || false
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NXF_CLOUDCACHE_PATH=gs://rnaseq-nf/cache \
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$NXF_CMD -trace nextflow,io.seqera -C ./google.config \
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run nextflow-io/rnaseq-nf \
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-with-report \
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-with-trace $OPTS \
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-plugins nf-cloudcache
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[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
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NXF_CLOUDCACHE_PATH=gs://rnaseq-nf/cache \
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$NXF_CMD -trace nextflow,io.seqera -C ./google.config \
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run nextflow-io/rnaseq-nf \
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-with-report \
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-with-trace $OPTS \
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-plugins nf-cloudcache \
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-resume
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[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
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[[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false
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## Test job array with Fusion
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$NXF_CMD -C ./google.config \
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run nextflow-io/hello \
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-process.array 10 \
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-with-wave \
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-with-fusion
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## Test job array
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$NXF_CMD -C ./google.config \
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run nextflow-io/hello \
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-process.array 10
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