add nextflow d30e48d

nextflow/validation/await.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+set -eu
+
+TIMEOUT=3600    # terminate after one hour
+KEEPALIVE=480   # time after which print an output to keep alive travis
+
+# launch main command to await  
+( "$@" | tee stdout.log ) &
+pid=$!
+
+# make sure to terminate target command on exit
+trap "kill $pid" TERM INT USR1 USR2
+
+# monitor task execution 
+begin=$(date +%s)
+size=0
+while kill -0 $pid > /dev/null 2>&1; do 
+    sleep 1
+
+    # continue to await if there's a change 
+    # in the stdout file 
+    ### BSD current=$(stat -f%z stdout.log)
+    current=$(stat -c '%s' stdout.log)
+    if [[ $current != $size ]]; then
+      size=$current
+      begin=$(date +%s)
+      continue
+    fi
+
+    # kill the execution if it's taking too 
+    # much time without producing any output
+    now=$(date +%s)
+    delta=$((now-begin))
+    if ((delta>=$TIMEOUT)); then
+        echo Taking too long ... killing it!
+        kill $pid
+        exit 1
+    elif ((delta>=$KEEPALIVE)); then    
+        echo "[keep alive]"
+    fi  
+done

nextflow/validation/awsbatch-unstage-fail.config

@@ -0,0 +1,12 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+
+workDir = 's3://nextflow-ci/work'
+process.executor = 'awsbatch'
+process.queue = 'nextflow-ci'
+process.container = 'quay.io/nextflow/test-aws-unstage-fail:1.0'
+aws.region = 'eu-west-1'
+aws.batch.maxTransferAttempts = 3 
+aws.batch.delayBetweenAttempts = '5 sec'

nextflow/validation/awsbatch.config

@@ -0,0 +1,13 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+
+workDir = 's3://nextflow-ci/work'
+process.executor = 'awsbatch'
+process.queue = 'nextflow-ci'
+process.container = 'quay.io/nextflow/rnaseq-nf:latest'
+aws.region = 'eu-west-1'
+aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
+aws.batch.maxTransferAttempts = 3 
+aws.batch.delayBetweenAttempts = '5 sec'

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

nextflow/validation/awsfargate.config

@@ -0,0 +1,14 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+
+workDir = 's3://nextflow-ci/work'
+process.executor = 'awsbatch'
+process.queue = 'nextflow-fg'
+process.container = 'quay.io/nextflow/rnaseq-nf:latest'
+aws.region = 'eu-west-1'
+aws.batch.platformType = 'fargate'
+aws.batch.jobRole = 'arn:aws:iam::195996028523:role/nf-batchjobrole'
+aws.batch.executionRole = 'arn:aws:iam::195996028523:role/nf-batchexecutionrole'
+wave.enabled = true

nextflow/validation/azure.config

@@ -0,0 +1,25 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+
+process {
+  executor = 'azurebatch'
+  container = 'quay.io/nextflow/rnaseq-nf:v1.1'
+  queue = 'nextflow-ci'
+}
+
+workDir = 'az://my-data/work'
+
+azure {
+  batch {
+    location = 'westeurope'
+    allowPoolCreation = true
+    pools {
+      'nextflow-ci' {
+          autoScale = true
+      }
+    }
+  }
+}
+

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

nextflow/validation/google.config

@@ -0,0 +1,12 @@
+/*
+ * do not include plugin requirements otherwise latest
+ * published version will be downloaded instead of using local build
+ */
+params.array_file_path = "gs://nf-test-arrays/file" 
+params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
+params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
+params.multiqc = 'gs://rnaseq-nf/multiqc'
+process.executor = 'google-batch'
+process.container = 'quay.io/nextflow/rnaseq-nf:latest'
+process.machineType = "n1-standard-1"
+workDir = 'gs://rnaseq-nf/scratch'

nextflow/validation/google.sh

@@ -0,0 +1,80 @@
+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 ./google.config -q run ./test-arrays.nf > array_output
+[[ `grep 'Hi from the nf-test-array bucket!' -c array_output` == 3 ]] && echo OK || { echo 'Failed array tasks' && false; }
+
+
+$NXF_CMD -C ./google.config \
+    run ./test-readspair.nf \
+    -with-report \
+    -with-trace $OPTS
+
+## complex paths test
+$NXF_CMD -C ./google.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
+$NXF_CMD -C ./google.config run ./test-complexpaths.nf -resume
+[[ -d foo ]] || false
+[[ -e 'foo/.alpha' ]] || false
+[[ -e 'foo/01_A(R1).fastq' ]] || false
+[[ -e 'foo/01_A(R2).fastq' ]] || false
+[[ -e 'foo/f1.fa' ]] || false
+[[ -e 'foo/f2.fa' ]] || false
+[[ -e 'foo/f3.fa' ]] || false
+[[ -e 'foo/hello.txt' ]] || false
+[[ -e 'foo/sample.html' ]] || false
+[[ -e 'foo/sample.zip' ]] || false
+[[ -e 'foo/sample_(1 2).vcf' ]] || false
+
+NXF_CLOUDCACHE_PATH=gs://rnaseq-nf/cache \
+$NXF_CMD -trace nextflow,io.seqera -C ./google.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -plugins nf-cloudcache
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+
+NXF_CLOUDCACHE_PATH=gs://rnaseq-nf/cache \
+$NXF_CMD -trace nextflow,io.seqera -C ./google.config \
+    run nextflow-io/rnaseq-nf \
+    -with-report \
+    -with-trace $OPTS \
+    -plugins nf-cloudcache \
+    -resume
+[[ `grep -c 'Using Nextflow cache factory: nextflow.cache.CloudCacheFactory' .nextflow.log` == 1 ]] || false
+[[ `grep -c 'Cached process > ' .nextflow.log` == 4 ]] || false
+
+## Test job array with Fusion
+$NXF_CMD -C ./google.config \
+    run nextflow-io/hello \
+    -process.array 10 \
+    -with-wave \
+    -with-fusion
+    
+## Test job array
+$NXF_CMD -C ./google.config \
+    run nextflow-io/hello \
+    -process.array 10
+
+

nextflow/validation/test-arrays.nf

@@ -0,0 +1,20 @@
+process python_version {
+    array 3
+    input:
+    val x
+    path input_file
+
+    output:
+    stdout
+
+    script:
+    """
+    echo $x
+    cat $input_file
+    """
+}
+
+workflow {
+    python_version(channel.of(1,2,3), params.array_file_path) | view
+}
+

nextflow/validation/test-aws-unstage-fail-container/Dockerfile

@@ -0,0 +1,11 @@
+FROM ubuntu
+
+RUN apt-get update && apt-get -y install curl unzip && apt-get clean
+
+
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && ./aws/install && rm -rf aws*
+
+ADD fake_aws /fake_aws
+
+ENV PATH=/fake_aws/bin/:$PATH

nextflow/validation/test-aws-unstage-fail-container/fake_aws/bin/aws

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+if [[ "$*" == *".command."* ]] || [[ "$*" == *".exitcode"* ]]; then
+   /usr/local/bin/aws $@
+else
+   >&2 echo "Producing a failure in aws $@"
+   exit 2
+fi
+

nextflow/validation/test-aws-unstage-fail.nf

@@ -0,0 +1,16 @@
+process test {
+  input: 
+	val i
+  output: 
+        file("test${i}")
+        file("test_2_${i}")
+  script:
+  """
+  dd if=/dev/urandom of=test${i} bs=1K count=90
+  dd if=/dev/urandom of=test_2_${i} bs=1K count=90
+  """
+}
+
+workflow {
+  channel.of(1) | test
+}

nextflow/validation/test-complexpaths.nf

@@ -0,0 +1,43 @@
+workflow {
+    foo | mix | collect | bar
+}
+
+process foo {
+  publishDir 'foo'
+  container 'debian:latest'
+  output:
+  file '*.fa'
+  file 'hello.txt'
+  file '*.{zip,html}'
+  file '01_A(R{1,2}).fastq'
+  file 'sample_(1 2).vcf'
+  file '.alpha'
+
+  script:
+  """
+  echo A > hello.txt
+  echo B > sample.zip 
+  echo C > sample.html
+  echo D > 01_A\\(R1\\).fastq
+  echo E > 01_A\\(R2\\).fastq
+  echo F > sample_\\(1\\ 2\\).vcf
+  echo 1 > f1.fa
+  echo 2 > f2.fa
+  echo 3 > f3.fa
+  mkdir .alpha
+  echo "Hello world!" > .alpha/hello.txt
+  """
+}
+
+process bar {
+  debug true
+  container 'debian:latest'
+  input: 
+  file '*'
+
+  script:
+  """
+  cat .alpha/hello.txt
+  [ `cat * | grep -c ''` == 9 ] || false
+  """
+}

nextflow/validation/test-overwrite.nf

@@ -0,0 +1,15 @@
+workflow {
+  foo()
+}
+
+process foo {
+  container 'quay.io/nextflow/bash'
+  publishDir "gs://rnaseq-nf/scratch/tests", overwrite: true
+  output:
+  path 'hello.txt'
+
+  script:
+  """
+  touch hello.txt
+  """
+}

nextflow/validation/test-readspair.nf

@@ -0,0 +1,19 @@
+workflow {
+    reads_pair()
+    reads_pair
+        .out.view()
+        .collect()
+        .subscribe { assert it.name == ['test.R1.fastq','test.R2.fastq'] }
+}
+
+process reads_pair {
+    output:
+      file("reads/*")
+
+    script:
+      """
+      mkdir reads
+      touch reads/test.R1.fastq reads/test.R2.fastq
+      """
+}
+

nextflow/validation/test-subdirs.nf

@@ -0,0 +1,63 @@
+workflow {
+  foo | bar
+}
+
+process foo {
+    output:
+    path 'gsfolder/'
+    path 'gsfolder2'
+    path 'gsfolder3'
+    path 'gsfolder4'
+    path 'test5.txt'
+    path 'test6.txt'
+    path 'test7.txt'
+    path 'gsfolder5/sub'
+
+    script:
+    """
+    mkdir -p gsfolder/sub
+    touch gsfolder/test1.txt
+    touch gsfolder/sub/test1.txt
+
+    mkdir gsfolder2
+    touch gsfolder2/test2.txt
+
+    mkdir gsfolder3
+    touch gsfolder3/test3.txt
+
+    mkdir gsfolder4
+    touch gsfolder4/test4.txt
+
+    echo 'Hello 5'>>test5.txt
+    echo 'Hello 6'>>test6.txt
+    echo 'Hello 7'>>test7.txt
+
+    mkdir -p gsfolder5/sub
+    touch gsfolder5/sub/test8.txt
+    """
+}
+
+process bar {
+    input:
+    path test_folder
+    path test_folder2
+    path 'test-folder3'
+    path 'test-folder4/*'
+    path test5
+    path 'this-is-test-6.txt'
+    path 'test7/foo/*'
+    path 'test8/*'
+
+    script:
+    """
+    set -x
+    [[ -f $test_folder/test1.txt ]] || false
+    [[ -f $test_folder/sub/test1.txt ]] || false
+    [[ -f $test_folder2/test2.txt ]] || false
+    [[ -f test-folder3/test3.txt ]] || false
+    [[ -f test-folder4/gsfolder4/test4.txt ]] || false
+    [[ \$(cat $test5) = 'Hello 5' ]] || false
+    [[ \$(cat this-is-test-6.txt) = 'Hello 6' ]] || false
+    [[ \$(cat test7/foo/test7.txt) = 'Hello 7' ]] || false
+    """
+}

nextflow/validation/test.sh

@@ -0,0 +1,126 @@
+#!/bin/bash 
+set -e 
+
+get_abs_filename() {
+  echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
+}
+
+export NXF_IGNORE_WARN_DSL2=true
+export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
+# disable ansi log to make log more readable
+export NXF_ANSI_LOG=false
+export NXF_DISABLE_CHECK_LATEST=true
+
+test_integration() {
+    (
+      cd "$1"
+      sudo bash cleanup.sh
+      cd checks
+      bash run.sh
+    )
+}
+
+test_e2e() {
+    if [[ $TEST_SMOKE == true ]]; then
+      echo Skipping tests since TEST_SMOKE flag is true
+      exit 0
+    fi
+
+    #
+    # Hello
+    #
+    git clone https://github.com/nextflow-io/hello
+    (
+      cd hello
+      $NXF_CMD run .
+      $NXF_CMD run . -resume
+    )
+
+    #
+    # RNASEQ-NF
+    #
+    echo nextflow-io/rnaseq-nf
+    [[ $TOWER_ACCESS_TOKEN ]] && OPTS='-with-tower' || OPTS=''
+    $NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS
+    $NXF_CMD run nextflow-io/rnaseq-nf -with-docker $OPTS -resume
+}
+
+#
+# Integration tests
+#
+if [[ $TEST_MODE == 'test_integration' ]]; then
+  export NXF_SYNTAX_PARSER=v1
+  test_integration ../tests/
+  test_integration ../tests-v1/
+  test_e2e
+fi
+
+#
+# Integration tests (strict syntax)
+#
+if [[ $TEST_MODE == 'test_parser_v2' ]]; then
+  export NXF_SYNTAX_PARSER=v2
+  test_integration ../tests/
+  test_e2e
+fi
+
+#
+# Documentation tests
+#
+if [[ $TEST_MODE == 'test_docs' ]]; then
+
+    (
+      echo "Documentation tests"
+      cd ../docs/snippets/
+      bash test.sh
+    )
+
+fi
+
+#
+# AWS Batch tests
+#
+if [[ $TEST_MODE == 'test_aws' ]]; then
+    if [ "$AWS_ACCESS_KEY_ID" ]; then
+      echo "AWS batch tests"
+      bash awsbatch.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing AWS_ACCESS_KEY_ID variable -- Skipping AWS Batch tests"
+    fi
+fi
+
+#
+# Azure Batch tests
+#
+if [[ $TEST_MODE == 'test_azure' ]]; then
+    if [ "$AZURE_BATCH_ACCOUNT_KEY" ]; then
+      echo "Azure batch tests"
+      bash azure.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing AZURE_BATCH_ACCOUNT_KEY variable -- Skipping Azure Batch tests"
+    fi
+fi
+
+#
+# Google Batch
+#
+if [[ $TEST_MODE == 'test_google' ]]; then
+    if [ "$GOOGLE_SECRET" ]; then
+      echo "Google Batch tests"
+      bash google.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing GOOGLE_SECRET variable -- Skipping Google Batch tests"
+    fi
+fi
+
+#
+# Wave
+#
+if [[ $TEST_MODE == 'test_wave' ]]; then
+    if [ "$TOWER_ACCESS_TOKEN" ]; then
+      echo "Wave tests"
+      bash wave.sh
+    else
+      echo "::warning file=$0,line=$LINENO::Missing TOWER_ACCESS_TOKEN variable -- Skipping Wave tests"
+    fi
+fi

nextflow/validation/wave-tests/example1/demo.nf

@@ -0,0 +1,13 @@
+process foo {
+  container 'docker.io/pditommaso/my-secret-container:latest'
+  debug true
+
+  script:
+  """
+  my-secret-script.sh
+  """
+}
+
+workflow { 
+  foo()
+}

nextflow/validation/wave-tests/example1/nextflow.config

@@ -0,0 +1,4 @@
+docker {
+  enabled = true 
+} 
+

nextflow/validation/wave-tests/example1/run.sh

@@ -0,0 +1 @@
+$NXF_CMD run demo.nf -with-wave

nextflow/validation/wave-tests/example2/demo.nf

@@ -0,0 +1,7 @@
+include { hello } from './modules/foo'
+
+workflow {
+  hello()
+}
+
+

nextflow/validation/wave-tests/example2/modules/foo/Dockerfile

@@ -0,0 +1,7 @@
+FROM alpine 
+
+RUN apk update && apk add bash cowsay \
+        --update-cache \
+        --repository https://alpine.global.ssl.fastly.net/alpine/edge/community \
+        --repository https://alpine.global.ssl.fastly.net/alpine/edge/main \
+        --repository https://dl-3.alpinelinux.org/alpine/edge/testing

nextflow/validation/wave-tests/example2/modules/foo/main.nf

@@ -0,0 +1,8 @@
+process hello {
+  debug true
+  script:
+  """
+  cowsay Hello Summit! 
+  """
+}
+

nextflow/validation/wave-tests/example2/nextflow.config

@@ -0,0 +1,5 @@
+docker { 
+  enabled = true
+} 
+
+

nextflow/validation/wave-tests/example2/run.sh

@@ -0,0 +1,2 @@
+$NXF_CMD run demo.nf -with-wave
+

nextflow/validation/wave-tests/example3/demo.nf

@@ -0,0 +1,13 @@
+process cow {
+  debug true
+  conda 'cowpy=1.1.5'
+
+  script:
+  '''
+  echo cowpy 'Hello Spack'
+  '''
+}
+
+workflow {
+  cow()
+}

nextflow/validation/wave-tests/example3/nextflow.config

@@ -0,0 +1,9 @@
+wave {
+  enabled = true
+  strategy = ['conda']
+  build.repository = 'docker.io/pditommaso/wave-tests'
+}
+
+docker {
+  enabled = true
+}

nextflow/validation/wave-tests/example3/run.sh

@@ -0,0 +1,2 @@
+$NXF_CMD run demo.nf -with-wave
+

nextflow/validation/wave-tests/example4/demo.nf

@@ -0,0 +1,13 @@
+process cow {
+  debug true
+  conda 'https://prefix.dev/envs/pditommaso/wave/conda-lock.yml'
+
+  script:
+  '''
+  echo cowpy 'Hello Spack'
+  '''
+}
+
+workflow {
+  cow()
+}

nextflow/validation/wave-tests/example4/run.sh

@@ -0,0 +1,2 @@
+$NXF_CMD run demo.nf -with-wave
+

nextflow/validation/wave-tests/example6/nextflow.config

@@ -0,0 +1,13 @@
+docker {
+  enabled = true
+  envWhitelist = 'AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY'
+}
+
+fusion {
+  enabled = true
+}
+
+wave {
+  build.template = 'conda/pixi:v1'
+}
+

nextflow/validation/wave-tests/example6/run-aws.sh

@@ -0,0 +1,7 @@
+$NXF_CMD run \
+    rnaseq-nf \
+    -profile batch,s3-data \
+    -with-wave \
+    -with-fusion \
+    -process.scratch false
+

nextflow/validation/wave-tests/example6/run-gcp.sh

@@ -0,0 +1,7 @@
+$NXF_CMD run \
+    rnaseq-nf \
+    -profile google-batch,gs-data \
+    -with-wave \
+    -with-fusion \
+    -process.scratch false
+

nextflow/validation/wave-tests/example6/run.sh

@@ -0,0 +1,5 @@
+$NXF_CMD run \
+    rnaseq-nf \
+    -with-wave \
+    -w s3://nextflow-ci/wave
+

nextflow/validation/wave.sh

@@ -0,0 +1,28 @@
+set -e
+
+get_abs_filename() {
+  echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
+}
+
+export NXF_CMD=${NXF_CMD:-$(get_abs_filename ../launch.sh)}
+
+echo "Test Wave accessing private container repository"
+(cd wave-tests/example1; bash run.sh)
+
+echo "Test Wave building a container"
+(cd wave-tests/example2; bash run.sh)
+
+echo "Test Wave building from Conda package"
+(cd wave-tests/example3; bash run.sh)
+#
+#echo "Test Wave building from Conda lock file"
+#(cd wave-tests/example4; bash run.sh)
+
+echo "Test Wave running rnaseq-nf with Fusion on local executor"
+(cd wave-tests/example6; bash run.sh)
+
+echo "Test Wave running rnaseq-nf with Fusion on AWS Batch"
+(cd wave-tests/example6; bash run-aws.sh)
+
+echo "Test Wave running rnaseq-nf with Fusion on Google Batch"
+(cd wave-tests/example6; bash run-gcp.sh)