add nextflow d30e48d

nextflow/validation/awsbatch.sh

@@ -0,0 +1,83 @@
+#!/bin/bash
+set -e 
+
+get_abs_filename() {
+  echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
+}
+
+export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
+
+# Execution should fail ignoring
+$NXF_CMD run test-aws-unstage-fail.nf -c awsbatch-unstage-fail.config || true
+[[ `grep -c "Error executing process > 'test (1)'" .nextflow.log` == 1 ]] || false
+[[ `grep -c "  Essential container in task exited" .nextflow.log` == 1 ]] || false
+[[ `grep -cozP "Command exit status:\n  1" .nextflow.log` == 1 ]] || false
+[[ `grep -c "Producing a failure in aws" .nextflow.log` == 2 ]] || false
+
+$NXF_CMD run test-complexpaths.nf -c awsbatch.config
+[[ -d foo ]] || false
+[[ -e 'foo/.alpha' ]] || false
+[[ -e 'foo/01_A(R1).fastq' ]] || false
+[[ -e 'foo/01_A(R2).fastq' ]] || false
+[[ -e 'foo/f1.fa' ]] || false
+[[ -e 'foo/f2.fa' ]] || false
+[[ -e 'foo/f3.fa' ]] || false
+[[ -e 'foo/hello.txt' ]] || false
+[[ -e 'foo/sample.html' ]] || false
+[[ -e 'foo/sample.zip' ]] || false
+[[ -e 'foo/sample_(1 2).vcf' ]] || false
+
+rm -rf foo
+$NXF_CMD run test-complexpaths.nf -resume -c awsbatch.config
+[[ -d foo ]] || false
+[[ -e 'foo/.alpha' ]] || false
+[[ -e 'foo/01_A(R1).fastq' ]] || false
+[[ -e 'foo/01_A(R2).fastq' ]] || false
+[[ -e 'foo/f1.fa' ]] || false
+[[ -e 'foo/f2.fa' ]] || false
+[[ -e 'foo/f3.fa' ]] || false
+[[ -e 'foo/hello.txt' ]] || false
+[[ -e 'foo/sample.html' ]] || false
+[[ -e 'foo/sample.zip' ]] || false
+[[ -e 'foo/sample_(1 2).vcf' ]] || false
+
+$NXF_CMD run test-subdirs.nf -c awsbatch.config
+
+NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
+$NXF_CMD run nextflow-io/rnaseq-nf \
+    -profile batch \
+    -with-report \
+    -with-trace \
+    -plugins nf-cloudcache
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+
+NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
+$NXF_CMD run nextflow-io/rnaseq-nf \
+    -profile batch \
+    -with-report \
+    -with-trace \
+    -plugins nf-cloudcache \
+    -resume
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+[[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false
+
+## run with fargate + wave
+NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
+$NXF_CMD run nextflow-io/rnaseq-nf \
+    -profile batch \
+    -plugins nf-cloudcache,nf-wave \
+    -c awsfargate.config
+
+## Test use of job array
+NXF_CLOUDCACHE_PATH=s3://nextflow-ci/cache \
+$NXF_CMD run nextflow-io/hello \
+    -process.array 10 \
+    -plugins nf-cloudcache \
+    -c awsbatch.config
+
+## Test use of job array using Fusion
+$NXF_CMD run nextflow-io/hello \
+    -process.array 10 \
+    -with-wave \
+    -with-fusion \
+    -c awsbatch.config