add nextflow d30e48d

nextflow/validation/azure.sh

@@ -0,0 +1,65 @@
+set -e
+
+get_abs_filename() {
+  echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
+}
+
+export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
+
+
+[[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
+set -x
+$NXF_CMD -C ./azure.config \
+    run ./test-readspair.nf \
+    -with-report \
+    -with-trace $OPTS
+
+## complex paths test
+$NXF_CMD -C ./azure.config run ./test-complexpaths.nf
+# validate
+[[ -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
+$NXF_CMD -C ./azure.config run ./test-complexpaths.nf -resume
+[[ -d foo ]] || false
+[[ -e 'foo/.alpha' ]] || false
+[[ -e 'foo/01_A(R1).fastq' ]] || false
+[[ -e 'foo/01_A(R2).fastq' ]] || false
+[[ -e 'foo/f1.fa' ]] || false
+[[ -e 'foo/f2.fa' ]] || false
+[[ -e 'foo/f3.fa' ]] || false
+[[ -e 'foo/hello.txt' ]] || false
+[[ -e 'foo/sample.html' ]] || false
+[[ -e 'foo/sample.zip' ]] || false
+[[ -e 'foo/sample_(1 2).vcf' ]] || false
+
+## run test-subdirs inputs/outputs
+$NXF_CMD -C ./azure.config run ./test-subdirs.nf
+
+NXF_CLOUDCACHE_PATH=az://my-data/cache \
+$NXF_CMD -C ./azure.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -plugins nf-cloudcache
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+
+NXF_CLOUDCACHE_PATH=az://my-data/cache \
+$NXF_CMD -C ./azure.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -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