84 lines
2.6 KiB
Bash
84 lines
2.6 KiB
Bash
#!/bin/bash
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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:-$(get_abs_filename ../launch.sh)}
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# Execution should fail ignoring
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$NXF_CMD run test-aws-unstage-fail.nf -c awsbatch-unstage-fail.config || true
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[[ `grep -c "Error executing process > 'test (1)'" .nextflow.log` == 1 ]] || false
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[[ `grep -c " Essential container in task exited" .nextflow.log` == 1 ]] || false
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[[ `grep -cozP "Command exit status:\n 1" .nextflow.log` == 1 ]] || false
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[[ `grep -c "Producing a failure in aws" .nextflow.log` == 2 ]] || false
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$NXF_CMD run test-complexpaths.nf -c awsbatch.config
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[[ -d foo ]] || false
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[[ -e 'foo/.alpha' ]] || false
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[[ -e 'foo/01_A(R1).fastq' ]] || false
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[[ -e 'foo/01_A(R2).fastq' ]] || false
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[[ -e 'foo/f1.fa' ]] || false
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[[ -e 'foo/f2.fa' ]] || false
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[[ -e 'foo/f3.fa' ]] || false
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[[ -e 'foo/hello.txt' ]] || false
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[[ -e 'foo/sample.html' ]] || false
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[[ -e 'foo/sample.zip' ]] || false
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[[ -e 'foo/sample_(1 2).vcf' ]] || false
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rm -rf foo
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$NXF_CMD run test-complexpaths.nf -resume -c awsbatch.config
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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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$NXF_CMD run test-subdirs.nf -c awsbatch.config
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NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
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$NXF_CMD run nextflow-io/rnaseq-nf \
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-profile batch \
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-with-report \
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-with-trace \
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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=s3://nextflow-ci/cache \
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$NXF_CMD run nextflow-io/rnaseq-nf \
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-profile batch \
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-with-report \
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-with-trace \
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-plugins nf-cloudcache \
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-resume
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[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
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[[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false
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## run with fargate + wave
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NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
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$NXF_CMD run nextflow-io/rnaseq-nf \
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-profile batch \
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-plugins nf-cloudcache,nf-wave \
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-c awsfargate.config
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## Test use of job array
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NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
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$NXF_CMD run nextflow-io/hello \
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-process.array 10 \
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-plugins nf-cloudcache \
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-c awsbatch.config
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## Test use of job array using Fusion
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$NXF_CMD 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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-c awsbatch.config
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