add nextflow d30e48d

nextflow/tests/.gitignore

@@ -0,0 +1,8 @@
+.cache
+.nextflow.*
+results
+scratch
+work
+**/checks.out
+**/.stdout
+**/stdout

nextflow/tests/Dockerfile

@@ -0,0 +1,42 @@
+FROM pditommaso/dkrbase:1.2
+
+MAINTAINER Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+
+RUN apt-get update -y && apt-get install -q -y gnuplot python && apt-get clean 
+
+#
+# Required PERL modules
+#
+RUN cpanm Math::CDF Math::Round && \
+  rm -rf /root/.cpanm/work/
+
+
+#
+# BLAST
+#
+RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gz && \
+    tar xf ncbi-blast-2.2.29+-x64-linux.tar.gz && \
+    mv ncbi-blast-2.2.29+ /opt/ && \
+    rm -rf ncbi-blast-2.2.29+-x64-linux.tar.gz && \
+    ln -s /opt/ncbi-blast-2.2.29+/ /opt/blast
+
+# 
+# install T-Coffee 
+#
+RUN wget -q http://tcoffee.org/Packages/Stable/Version_11.00.8cbe486/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz && \
+  tar xf T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz -C /opt && \
+  mv /opt/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64 /opt/tcoffee && \
+  rm -rf /opt/tcoffee/plugins/linux/*  && \
+  rm T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz 
+
+#
+# Add AMPA script to bin folder 
+#
+ADD bin/AMPA.pl /usr/local/bin/
+
+
+#
+# Configure the env
+#
+ENV PATH="$PATH:/opt/ncbi-blast-2.2.29+/bin:/opt/tcoffee/bin"
+

nextflow/tests/README.md

@@ -0,0 +1,5 @@
+# Nextflow tests
+
+This repository contains the integration tests for Nextflow.
+
+![Nextflow CI](https://github.com/nextflow-io/nextflow/workflows/Nextflow%20CI/badge.svg)

nextflow/tests/agent-output-error.nf

@@ -0,0 +1,20 @@
+#!/usr/bin/env nextflow
+workflow {
+    FAIL()
+}
+
+
+/*
+ * Test for agent output mode error handling (NXF_AGENT_MODE=true)
+ * 
+ * This test verifies the error output format in agent mode.
+ * Run with: NXF_AGENT_MODE=true nextflow run agent-output-error.nf
+ */
+
+process FAIL {
+    script:
+    """
+    echo "Error message here" >&2
+    exit 127
+    """
+}

nextflow/tests/agent-output.nf

@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+workflow {
+    HELLO | WORLD | view
+}
+
+
+/*
+ * Test for agent output mode (NXF_AGENT_MODE=true)
+ * 
+ * This test verifies the minimal agent-friendly output format.
+ * Run with: NXF_AGENT_MODE=true nextflow run agent-output.nf
+ */
+
+process HELLO {
+    output:
+    stdout
+
+    script:
+    """
+    echo "Hello from agent mode"
+    """
+}
+
+process WORLD {
+    input:
+    val msg
+
+    output:
+    stdout
+
+    script:
+    """
+    echo "World received: ${msg}"
+    """
+}

nextflow/tests/ampa.nf

@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow 
+
+params.in = "$baseDir/data/sample.fa"
+
+
+/*
+ * For each sequence that is sent over the 'seq' channel
+ * the below task is executed
+ */
+process ampaTask {
+
+    input:
+    path seq
+
+    output:
+    path 'result'
+
+    // The BASH script to be executed - for each - sequence
+    script:
+    """
+    AMPA.pl -in=${seq} -noplot -rf=result -df=data
+    """
+
+}
+
+workflow {
+    channel.fromPath(params.in) |
+            splitFasta(file:true) |
+            ampaTask |
+            view { it.text }
+}
+

nextflow/tests/basic.nf

@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+/* 
+ * Command line input parameter 
+ */
+params.in = "$baseDir/data/sample.fa"
+
+
+/* 
+ * split a fasta file in multiple files 
+ */
+process splitSequences {
+
+    input:
+    path 'input.fa'
+
+    output:
+    path 'seq_*'
+
+    script:
+    """
+    awk '/^>/{f="seq_"++d} {print > f}' < input.fa
+    """
+
+}
+
+/* 
+ * Simple reverse the sequences 
+ */
+process reverse {
+
+    input:
+    path x
+    
+    output:
+    stdout
+
+    script:
+    """
+    cat $x | rev
+    """
+}
+
+
+workflow {
+    splitSequences(params.in) | reverse | view
+}
+

nextflow/tests/bin/AMPA.pl

@@ -0,0 +1,334 @@
+#!/usr/bin/perl -w
+use strict;
+use Math::CDF;
+use Math::Round;
+
+#
+# The default input parameters 
+# 
+my $debug = 0;
+my $noplot = 0;
+my $gnuplot = "";
+my $input_file = "protein.txt";
+my $window_size = 7;
+my $threshold = 0.225;
+my $graph_file = "";
+my $result_file = "results.$$";
+my $data_file = "sliding.$$";
+my $_prompt = "";
+
+#
+# Find out gnuplot 
+#
+
+if( exists $ENV{GNUPLOT_BIN}) { 
+        $gnuplot = $ENV{GNUPLOT_BIN};
+}
+if( $gnuplot eq "" ) { 
+        $gnuplot = `which gnuplot`;
+        chomp($gnuplot);
+}
+if( $gnuplot eq "" ) { 
+        print "AMPA requires gnuplot to be installed on your system.";
+        exit 2;
+}
+
+#
+# Parse the command 
+# 
+
+my $cl=join( " ", @ARGV);
+
+if (($cl=~/-h/) ||($cl=~/-H/) ) {
+        # print usage 
+        print "Usage: AMPA.pl -in=<input fasta file> [other options]\n";
+        print "\n";
+        print "Available options:\n";
+        print "-in      Fasta sequence input file\n";
+        print "-t       Threshold value (default: 7)\n";
+        print "-w       Window size value (default: 0.225)\n";
+        print "-rf      File where store the program result\n";
+        print "-df      File where store the produced plot data\n";
+        print "-gf      File where store the generated plot\n";
+        print "-noplot  Skip plot creation step\n";
+        exit 1;
+}
+
+#
+# If not command line is provided switch to interactive mode 
+#
+
+if ($#ARGV==-1 ) { 
+        # the input file name
+        print "Enter the name of the sequence file and then press Enter [$input_file]: ";
+        $_prompt = <STDIN>;
+        chomp($_prompt);
+        if( $_prompt ne "" ) { $input_file=$_prompt };
+
+        # the window size
+        print "Enter the desired window size as an odd number and then press Enter [$window_size]: ";
+        $_prompt = <STDIN>;
+        chomp($_prompt);
+        if( $_prompt ne "" ) { $window_size = $_prompt };
+        
+        # the threshold
+        print "Enter the desired threshold and then press Enter [$threshold]: ";
+        $_prompt = <STDIN>;
+        chomp($_prompt);
+        if( $_prompt ne "" ) { $threshold = $_prompt };
+}
+
+
+# option '-in': input file name
+if ( ($cl=~/-in=\s*(\S+)/)) { 
+        $input_file = $1;
+}
+
+# option '-w': window size
+if ( ($cl =~ /-w=\s*(\S+)/)) { 
+        $window_size = $1;
+}
+
+# option '-t': threshold value
+if ( ($cl =~ /-t=\s*(\S+)/)) { 
+        $threshold = $1;
+}
+
+# option '-gf': output graph file
+if ( ($cl =~ /-gf=\s*(\S+)/)) { 
+        $graph_file = $1;
+}
+
+# option '-rf': output result file
+if ( ($cl =~ /-rf=\s*(\S+)/)) { 
+        $result_file = $1;
+}
+
+# option '-df': output sliding file
+if ( ($cl =~ /-df=\s*(\S+)/)) { 
+        $data_file = $1;
+}
+
+# option '-debug': enable debug mode
+if ( ($cl =~ /-debug/)) { 
+        $debug = 1;
+}
+
+# option '-noplot': threshold value
+if ( ($cl =~ /-noplot/)) { 
+        $noplot = 1;
+}
+
+if( $debug != 0 ) { 
+        print "Window size      : $window_size\n";
+        print "Threshold value  : $threshold\n";
+        print "Input file name  : $input_file\n";
+        print "Graph file name  : $graph_file\n";
+        print "Result file name : $result_file\n";
+        print "Data file name   : $data_file\n";
+        print "Gnuplot bin      : $gnuplot\n";
+}
+
+#
+#  Main script start here 
+# 
+
+my(@names,@lengths,@sequences,$sequence_number,$protein);
+
+open(PROTEIN, "$input_file") or die "Cannot open '$input_file': $!\n";  
+
+#The program should read the user input sequence
+
+$/ = ">";
+
+for(my $c=1; $c<(($window_size + 1)/2); $c++) {
+    push (@sequences, 'X');
+    }
+
+while (my $sequence_record = <PROTEIN>) {
+    if ($sequence_record eq ">") {
+        next;
+    }
+
+    my $sequence_name = "";
+    if ($sequence_record =~ m/([^\n]+)/) {
+        $sequence_name = $1;
+    } else {
+        $sequence_name = "No title was found!";
+    }
+
+    $sequence_record =~ s/[^\n]+//;
+    push (@names, $sequence_name);
+    $sequence_record =~ s/[^ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]//g;    
+    push (@sequences, $sequence_record);
+    push (@lengths, length($sequence_record));
+    my $sequence_length = length($sequence_record);
+}
+
+for(my $c=1; $c<(($window_size + 1)/2); $c++) {
+    push (@sequences, 'X');
+}
+
+my $sequences = join("",@sequences);
+
+close(PROTEIN) or die "Cannot close the file: $!\n";
+
+#The program calls the subroutines to analyze the sequence
+
+&sliding($sequences);
+if(!$noplot) {
+	&gnuplot_sld();
+} 
+
+### Subroutines
+
+# Defines the value at the window center (window_size+1)/2
+
+sub sliding {
+    open(KD,">$data_file") or die("Could not open '$data_file': $!\n");
+    open(RS,">$result_file") or die("Could not open '$result_file': $!\n");
+    my($center,$length);
+    my $half = (($window_size + 1)/2);
+
+# These are the antimicrobial propensity values for each amino acid
+
+    my %sliding = (
+                          'A',    0.307,  
+                          'R',    0.106,  
+                          'N',    0.240,  
+                          'D',    0.479,  
+                          'C',    0.165,  
+                          'Q',    0.248,  
+                          'E',    0.449,  
+                          'G',    0.265,  
+                          'H',    0.202,  
+                          'I',    0.198,  
+                          'L',    0.246,  
+                          'K',    0.111,  
+                          'M',    0.265,  
+                          'F',    0.246,  
+                          'P',    0.327,  
+                          'S',    0.281,  
+                          'T',    0.242,  
+                          'W',    0.172,  
+                          'Y',    0.185,  
+                          'V',    0.200,
+              'X',      $threshold  
+                          );
+
+    $protein = shift;
+
+    print KD "# The window size is currently set at $window_size.\n";
+    print KD "# Here are the AMSI values for this protein:\n";
+    print KD "# $names[0]\n";
+    print KD "# Pos\ APV\n";
+    print KD "# ---\t-------------------\n";
+        
+        my $acc1=0;
+        my $acc2=0;
+        my $bacindex=0;
+        my $amvalue=0;
+    my $bacvalue=0;
+        my $prob=0;
+
+    for(my $i=0;$i<=(length($protein)-$window_size);$i++) {
+        my $window = substr($protein, $i, $window_size);
+        my $sum=0;
+        for(my $j=0; $j<$window_size; $j++) {
+            my $PV = 0;
+            my $residue = substr($window, $j, 1);
+            $PV = $sliding{$residue};
+            $sum+=$PV;
+        }
+    
+        $center = $i + $half;
+    my $position = $center - 3;
+        my $APV=$sum/$window_size;
+        $APV = sprintf "%.3f", $APV;
+        print KD "$position\t$APV\n";
+        $amvalue=$amvalue+$APV;
+
+                                if($acc1==3) {
+                                                if($acc2>=10){
+                                                        my $init=$position-$acc2-2;
+                                                        my $last=$position-1;
+                            my $bacvalue=(($bacvalue)/($last-$init+1));
+                            $prob = &Math::CDF::pnorm(($bacvalue-0.2584)/0.02479);
+                            $prob*=100;
+                            my $rbacvalue = nearest(.001, $bacvalue);                            
+                            my $rprob = nearest(1, $prob);
+                                                        print RS "Antimicrobial stretch found in $init to $last. Propensity value $rbacvalue ($rprob %) \n";
+                            $bacindex++;                                                        
+                            $acc2=0;
+                                                        $acc1=0;
+                            $bacvalue=0;
+                            $prob=0;
+                                                        }
+                                                if($acc2<10){
+                                                $acc1=0;
+                                                $acc2=0;
+                        $bacvalue=0;
+                                                }
+                                             }
+                                if($acc1!=3){
+                        if($acc2==0) {
+                            $acc1=0;
+                            $bacvalue=0;
+                        }                                                
+                        if($APV<=$threshold) {
+                                                $acc2++;
+                        $bacvalue+=$APV
+                                                }
+                                                if($APV>$threshold){
+                                                $acc1++;
+                        $bacvalue+=$APV
+                                                }
+                                            }
+                if($position==(length($protein)-(($window_size)-1)) && $acc2>=10) {
+                        my $init=$position-$acc2-2;
+                                                my $last=$position-1;
+                        my $bacvalue=(($bacvalue)/($last-$init+1));
+                        $bacindex++;
+                        $prob = &Math::CDF::pnorm(($bacvalue-0.2584)/0.02479);
+                        $prob*=100;
+                        my $rbacvalue = nearest(.001, $bacvalue);                            
+                        my $rprob = nearest(1, $prob);                                                
+                        print RS "Antimicrobial stretch found in $init to $last. Propensity value $rbacvalue ($rprob %) \n";    
+                        }
+
+
+}
+
+
+print RS "# This protein has $bacindex bactericidal stretches \n";
+my $manvalue = nearest(.001, $amvalue/(length($protein)-6));
+print RS "# This protein has a mean antimicrobial value of $manvalue \n";       
+   
+close(KD) or die("Could not close file: $!\n");
+}
+
+
+sub gnuplot_sld {
+    my $cmdline = "|$gnuplot -persist";
+   
+    open (GP, $cmdline) or die "no gnuplot";
+    # force buffer to flush after each write
+    use FileHandle;
+    GP->autoflush(1);
+
+    print GP "set title \"Antimicrobial Profile\"\n";
+    print GP "set xlabel \"Position\"\n";
+    print GP "set ylabel \"Score\"\n";
+    print GP "set grid\n";
+    print GP "set data style lines\n";
+
+        # if an output has been specified output to it 
+    if( $graph_file ne "" ) { 
+        print GP "set terminal png large enhanced  size 800 600\n";
+        print GP "set output '$graph_file' \n";
+    }
+    
+    print GP "plot \"$data_file\" u 1:2 t \"Antimicrobial profile \" w lines\n";
+    close GP;
+}
+

nextflow/tests/blast-db/tiny.psd

@@ -0,0 +1,94 @@
+1abo:a0
+1abo:b1
+1abo:c2
+1abo:d3
+1ihb:a4
+1ihb:b5
+1ihc:a6
+1ihd:a7
+1ihd:c8
+1ihf:a9
+1ihf:b10
+1ihf:c11
+1ihf:d12
+1ihf:e13
+1ihg:a14
+1ihh:a15
+1ihh:b16
+1ihi:a17
+1ihi:b18
+1ihm:a19
+1ihm:b20
+1ihm:c21
+1ihn:a22
+1ihn:b23
+1iho:a24
+1iho:b25
+1ihp:a26
+1ihq:a27
+1ihq:b28
+1ihr:a29
+1ihr:b30
+1ihs:h31
+1ihs:i32
+1ihs:l33
+1iht:h34
+1iht:i35
+1iht:l36
+1ihu:a37
+1ihv:a38
+1ihv:b39
+1ihw:a40
+1ihw:b41
+1ihz:a42
+1pht:a43
+1vie:a44
+1ycs:a45
+1ycs:b46
+lcl|1abo:a0
+lcl|1abo:b1
+lcl|1abo:c2
+lcl|1abo:d3
+lcl|1ihb:a4
+lcl|1ihb:b5
+lcl|1ihc:a6
+lcl|1ihd:a7
+lcl|1ihd:c8
+lcl|1ihf:a9
+lcl|1ihf:b10
+lcl|1ihf:c11
+lcl|1ihf:d12
+lcl|1ihf:e13
+lcl|1ihg:a14
+lcl|1ihh:a15
+lcl|1ihh:b16
+lcl|1ihi:a17
+lcl|1ihi:b18
+lcl|1ihm:a19
+lcl|1ihm:b20
+lcl|1ihm:c21
+lcl|1ihn:a22
+lcl|1ihn:b23
+lcl|1iho:a24
+lcl|1iho:b25
+lcl|1ihp:a26
+lcl|1ihq:a27
+lcl|1ihq:b28
+lcl|1ihr:a29
+lcl|1ihr:b30
+lcl|1ihs:h31
+lcl|1ihs:i32
+lcl|1ihs:l33
+lcl|1iht:h34
+lcl|1iht:i35
+lcl|1iht:l36
+lcl|1ihu:a37
+lcl|1ihv:a38
+lcl|1ihv:b39
+lcl|1ihw:a40
+lcl|1ihw:b41
+lcl|1ihz:a42
+lcl|1pht:a43
+lcl|1vie:a44
+lcl|1ycs:a45
+lcl|1ycs:b46

nextflow/tests/blast-parallel.nf

@@ -0,0 +1,66 @@
+#!/usr/bin/env nextflow
+
+params.db = "$baseDir/blast-db/tiny"
+params.query = "$baseDir/data/sample.fa"
+params.chunk = 1 
+
+/* 
+ * Extends a BLAST query for each entry in the 'chunks' channel 
+ */
+process blast {
+    input:
+    path 'query.fa'
+    val db
+
+    output:
+    path 'top_hits'
+
+    script:
+    """
+    blastp -db ${db} -query query.fa -outfmt 6 > blast_result
+    cat blast_result | head -n 10 | cut -f 2 > top_hits
+    """
+}
+
+/*
+ * Find out the top 10 matches returned by the BLAST query
+ */ 
+process extract {
+    input:
+    path 'top_hits'
+    path db
+
+    output:
+    path 'sequences'
+
+    script:
+    "blastdbcmd -db ${db} -entry_batch top_hits | head -n 10 > sequences"
+}
+
+
+/*
+ * Aligns a T-Coffee MSA and print it 
+ */
+process align {
+    debug true
+
+    input:
+    path all_seq
+
+    script:
+    "t_coffee $all_seq 2>/dev/null | tee align_result"
+}
+
+/*
+ * main flow
+ */
+workflow {
+    ch_fasta = channel.fromPath(params.query)
+        | splitFasta(by: params.chunk, file:true)
+
+    ch_sequences = blast(ch_fasta, params.db)
+
+    extract(ch_sequences, params.db)
+        | collectFile(name:'all_seq') // Collect all hits to a single file called  'all_seq'
+        | align
+}

nextflow/tests/blast.nf

@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+
+params.db = "$baseDir/blast-db/tiny"
+params.query = "$baseDir/data/sample.fa"
+params.chunkSize = 1
+
+process blast {
+    input:
+    path 'seq.fa'
+    val db
+
+    output:
+    path 'out'
+
+    script:
+    """
+    blastp -db $db -query seq.fa -outfmt 6 > out
+    """
+}
+
+process sort {
+    input:
+    path 'hits_*'
+
+    output:
+    stdout
+
+    script:
+    """
+    sort hits_*
+    """
+}
+
+
+workflow {
+    ch_fasta = channel.fromPath(params.query)
+        | splitFasta( by: params.chunkSize, file:true )
+
+    blast(ch_fasta, params.db)
+        | collect
+        | sort
+        | subscribe { hits -> println hits }
+}

nextflow/tests/buffer.nf

@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+process blastThemAll {
+    debug true
+
+    input:
+    path x
+
+    script:
+    """
+    echo $x
+    """
+}
+
+
+workflow {
+    Channel
+        .fromPath("$baseDir/data/p?.fa") |
+        toSortedList |
+        flatten |
+        buffer(size:2, remainder: true) |
+        blastThemAll
+}

nextflow/tests/cache-bak.nf

@@ -0,0 +1,9 @@
+workflow {
+  foo()
+}
+
+process foo {
+  debug true
+  script:
+  /echo Hello world/
+}

nextflow/tests/checks/.IGNORE

@@ -0,0 +1,2 @@
+# TEST TO BE IGNORED 
+plugin-registry.nf

nextflow/tests/checks/.IGNORE-DOCKER

@@ -0,0 +1,8 @@
+# TESTS TO BE IGNORED WHEN A DOCKER ENGINE 
+# IS NOT AVAILABLE
+ampa.nf
+blast.nf
+blast-parallel.nf
+env-container.nf
+env-container-with(special)chars.nf
+workdir-with-blank.nf

nextflow/tests/checks/.IGNORE-PARSER-V2

@@ -0,0 +1,14 @@
+# TESTS THAT SHOULD ONLY BE RUN BY THE V2 PARSER
+collect-record.nf
+dynamic-filename-typed.nf
+env-typed.nf
+eval-out-typed.nf
+nullable-path.nf
+output-dsl.nf
+params-dsl.nf
+record-types.nf
+records.nf
+task-ext-block.nf
+topic-channel-typed.nf
+type-annotations.nf
+workflow-oncomplete-v2.nf

nextflow/tests/checks/agent-output-error.nf/.checks

@@ -0,0 +1,47 @@
+#!/bin/bash
+#
+# Test agent output mode error handling (NXF_AGENT_MODE=true)
+#
+
+set -e
+
+# Run workflow with agent mode enabled (expect failure)
+NXF_AGENT_MODE=true $NXF_CMD -q run $NXF_SCRIPT > stdout.txt 2> stderr.txt && {
+    echo "ERROR: Workflow should have failed"
+    exit 1
+}
+
+# Verify agent output format contains error info
+if ! grep -q '\[PIPELINE\]' stdout.txt; then
+    echo "ERROR: Missing [PIPELINE] in agent output"
+    cat stdout.txt
+    exit 1
+fi
+
+if ! grep -q '\[ERROR\]' stdout.txt; then
+    echo "ERROR: Missing [ERROR] in agent output"
+    cat stdout.txt
+    exit 1
+fi
+
+if ! grep -q '\[FAILED\]' stdout.txt; then
+    echo "ERROR: Missing [FAILED] in agent output"
+    cat stdout.txt
+    exit 1
+fi
+
+# Verify error contains exit code
+if ! grep -q 'exit: 127' stdout.txt; then
+    echo "ERROR: Missing exit code in error output"
+    cat stdout.txt
+    exit 1
+fi
+
+# Verify error contains workdir
+if ! grep -q 'workdir:' stdout.txt; then
+    echo "ERROR: Missing workdir in error output"
+    cat stdout.txt
+    exit 1
+fi
+
+echo "Agent error output mode test passed"

nextflow/tests/checks/agent-output.nf/.checks

@@ -0,0 +1,46 @@
+#!/bin/bash
+#
+# Test agent output mode (NXF_AGENT_MODE=true)
+#
+
+set -e
+
+# Run workflow with agent mode enabled
+NXF_AGENT_MODE=true $NXF_CMD -q run $NXF_SCRIPT > stdout.txt 2> stderr.txt || true
+
+# Verify agent output format in stdout
+# Should contain [PIPELINE], [WORKDIR], and [SUCCESS] or [FAILED]
+
+if ! grep -q '\[PIPELINE\]' stdout.txt; then
+    echo "ERROR: Missing [PIPELINE] in agent output"
+    cat stdout.txt
+    exit 1
+fi
+
+if ! grep -q '\[WORKDIR\]' stdout.txt; then
+    echo "ERROR: Missing [WORKDIR] in agent output"
+    cat stdout.txt
+    exit 1
+fi
+
+if ! grep -q '\[SUCCESS\]' stdout.txt; then
+    echo "ERROR: Missing [SUCCESS] in agent output"
+    cat stdout.txt
+    exit 1
+fi
+
+# Verify banner is suppressed (should NOT contain "N E X T F L O W")
+if grep -q 'N E X T F L O W' stdout.txt; then
+    echo "ERROR: Banner should be suppressed in agent mode"
+    cat stdout.txt
+    exit 1
+fi
+
+# Verify workflow output is present
+if ! grep -q 'World received: Hello from agent mode' stdout.txt; then
+    echo "ERROR: Workflow stdout incorrect"
+    cat stdout.txt
+    exit 1
+fi
+
+echo "Agent output mode test passed"

nextflow/tests/checks/agent-output.nf/.expected

@@ -0,0 +1 @@
+World received: Hello from agent mode

nextflow/tests/checks/ampa.nf/.checks

@@ -0,0 +1,17 @@
+#
+# run normal mode 
+#
+$NXF_RUN $WITH_DOCKER --out result.txt | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 5 ]] || false
+cmp .expected <(sort .stdout) || false
+
+
+#
+# run resume mode 
+#
+$NXF_RUN $WITH_DOCKER --out result.txt -resume | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 5 ]] || false
+cmp .expected <(sort .stdout) || false
+

nextflow/tests/checks/ampa.nf/.expected

@@ -0,0 +1,15 @@
+
+
+
+
+
+# This protein has 0 bactericidal stretches 
+# This protein has 0 bactericidal stretches 
+# This protein has 0 bactericidal stretches 
+# This protein has 0 bactericidal stretches 
+# This protein has 0 bactericidal stretches 
+# This protein has a mean antimicrobial value of 0.235 
+# This protein has a mean antimicrobial value of 0.25 
+# This protein has a mean antimicrobial value of 0.251 
+# This protein has a mean antimicrobial value of 0.266 
+# This protein has a mean antimicrobial value of 0.28 

nextflow/tests/checks/basic.nf/.checks

@@ -0,0 +1,19 @@
+set -e
+
+#
+# run normal mode 
+#
+$NXF_RUN | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
+diff .expected .stdout || false
+
+
+#
+# run resume mode 
+#
+$NXF_RUN -resume | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
+diff .expected .stdout || false
+

nextflow/tests/checks/basic.nf/.expected

@@ -0,0 +1,15 @@
+Aoba1>
+SPVWGQGNKTQAECWEGNHNYGLVRLKEGKTISLTNDGSAVFDYLAVFLN
+NVPTIYN
+Bscy1>
+YGEKDNLRAWWWEIEDEDERHIITMCDGEKMPLEDDNQPEYDWLAYIVGK
+PYLGLLNRPV
+thp1>
+GIEEPRAEQGDSFGLAVLSGKNVTLIDGLHLDIDEEREKKYDYLARYQYG
+PSIKKRGIYEVYTGPFDGREGTTENYGNLW
+eiv1>
+IRELAAVPYIQVSGPHAESEVAYGEPTLNTCYWGVIQGQWAAGSKKRVRD
+N
+Avhi1>
+DRIIKAKRRPVVKIDSNDQIVVAGEGKWLLKAPGKWVPDRSDRYYVRFN
+

nextflow/tests/checks/blast-parallel.nf/.checks

@@ -0,0 +1,19 @@
+set -e
+
+#
+# run normal mode
+#
+$NXF_RUN $WITH_DOCKER > stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > blast'` == 5 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > extract'` == 5 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > align'` == 1 ]] || false
+
+#
+# run resume mode
+#
+$NXF_RUN $WITH_DOCKER -resume > stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process > blast'` == 5 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Cached process > extract'` == 5 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Cached process > align'` == 1 ]] || false

nextflow/tests/checks/blast-parallel.nf/.expected

@@ -0,0 +1,284 @@
+CLUSTAL FORMAT for T-COFFEE Version_11.00.8cbe486 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=338, Nseq=18, Len=694 
+
+lcl|1VIE_A      VF-------PS----NA---------------------------T-----
+lcl|1IHU_A      MQFL-----QNIPPY-LFFTGKGGVGKTSISCATAIRLAEQGKRVLLVST
+lcl|1ABO_B      MND------PN-----L---------------------------------
+lcl|1ABO_A      MND------PN-----L---------------------------------
+lcl|1YCS_B      PEITGQVSLPP---GKR---------------------------TNL---
+lcl|1IHD_C      LPN-------------I---------------------------------
+lcl|1IHW_B      MIQ-----------------------------------------------
+lcl|1IHW_A      MIQ-----------------------------------------------
+lcl|1IHV_B      MIQ-----------------------------------------------
+lcl|1IHV_A      MIQ-----------------------------------------------
+lcl|1YCS_A      SS-----SVPS----QK---------------------------T-----
+lcl|1PHT_A      MS------------------------------------------------
+lcl|1YCS_B_1    PEITGQVSLPP---GKR---------------------------TNL---
+lcl|1YCS_B_2    PEITGQVSLPP---GKR---------------------------TNL---
+lcl|1YCS_B_3    PEITGQVSLPP---GKR---------------------------TNL---
+lcl|1ABO_B_1    MND------PN-----L---------------------------------
+lcl|1ABO_A_1    MND------PN-----L---------------------------------
+lcl|1PHT_A_1    MS------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      -----------F------------------------GM-GDRVR------
+lcl|1IHU_A      DPASNVGQVFSQTIGNTIQAIASVPGLSALEIDPQAAAQQYRARIVDPIK
+lcl|1ABO_B      ----------------------------------------FVA-------
+lcl|1ABO_A      ----------------------------------------FVA-------
+lcl|1YCS_B      ------RKTGSER-----------------------IAHGMRVKF-----
+lcl|1IHD_C      ------------------------------------------------T-
+lcl|1IHW_B      ---------------------------------------NFRVYY-----
+lcl|1IHW_A      ---------------------------------------NFRVYY-----
+lcl|1IHV_B      ---------------------------------------NFRVYY-----
+lcl|1IHV_A      ---------------------------------------NFRVYY-----
+lcl|1YCS_A      -----------YQ-----------------------GSYGFRLGF-----
+lcl|1PHT_A      --------------------------------------------------
+lcl|1YCS_B_1    ------RKTGSER-----------------------IAHGMRVKF-----
+lcl|1YCS_B_2    ------RKTGSER-----------------------IAHGMRVKF-----
+lcl|1YCS_B_3    ------RKTGSER-----------------------IAHGMRVKF-----
+lcl|1ABO_B_1    ----------------------------------------FVA-------
+lcl|1ABO_A_1    ----------------------------------------FVA-------
+lcl|1PHT_A_1    --------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      --------------------------KKSGA-------------------
+lcl|1IHU_A      GVLPDDVVSSINEQLSGACTTEIAAFDE-FTGLLTDASLLTRFDHIIFDT
+lcl|1ABO_B      --------------------------------------------------
+lcl|1ABO_A      --------------------------------------------------
+lcl|1YCS_B      --------------------------NPLPLALLLDSSLEGEFDLV----
+lcl|1IHD_C      -------------------------------ILATGGTIAGGGDSA----
+lcl|1IHW_B      --------------------------------------------------
+lcl|1IHW_A      --------------------------------------------------
+lcl|1IHV_B      --------------------------------------------------
+lcl|1IHV_A      --------------------------------------------------
+lcl|1YCS_A      --------------------------LHSGTA------------------
+lcl|1PHT_A      --------------------------------------------------
+lcl|1YCS_B_1    --------------------------NPLPLALLLDSSLEGEFDLV----
+lcl|1YCS_B_2    --------------------------NPLPLALLLDSSLEGEFDLV----
+lcl|1YCS_B_3    --------------------------NPLPLALLLDSSLEGEFDLV----
+lcl|1ABO_B_1    --------------------------------------------------
+lcl|1ABO_A_1    --------------------------------------------------
+lcl|1PHT_A_1    --------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      APTGHTIRLLQLPGAWSSFIDSNPEGASCLGPMAGLEKQREQYAYAVEAL
+lcl|1ABO_B      --------------------------------------------------
+lcl|1ABO_A      --------------------------------------------------
+lcl|1YCS_B      --------------------------------------------------
+lcl|1IHD_C      --------------------------------------------------
+lcl|1IHW_B      --------------------------------------------------
+lcl|1IHW_A      --------------------------------------------------
+lcl|1IHV_B      --------------------------------------------------
+lcl|1IHV_A      --------------------------------------------------
+lcl|1YCS_A      --------------------------------------------------
+lcl|1PHT_A      --------------------------------------------------
+lcl|1YCS_B_1    --------------------------------------------------
+lcl|1YCS_B_2    --------------------------------------------------
+lcl|1YCS_B_3    --------------------------------------------------
+lcl|1ABO_B_1    --------------------------------------------------
+lcl|1ABO_A_1    --------------------------------------------------
+lcl|1PHT_A_1    --------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      SDPKRTRLVLVARLQKSTLQEVARTHLELAAIGLKNQYLVINGVLPKTEA
+lcl|1ABO_B      --------------------------------------------------
+lcl|1ABO_A      --------------------------------------------------
+lcl|1YCS_B      --------------------------------------------------
+lcl|1IHD_C      --------------------------------------------------
+lcl|1IHW_B      --------------------------------------------------
+lcl|1IHW_A      --------------------------------------------------
+lcl|1IHV_B      --------------------------------------------------
+lcl|1IHV_A      --------------------------------------------------
+lcl|1YCS_A      --------------------------------------------------
+lcl|1PHT_A      --------------------------------------------------
+lcl|1YCS_B_1    --------------------------------------------------
+lcl|1YCS_B_2    --------------------------------------------------
+lcl|1YCS_B_3    --------------------------------------------------
+lcl|1ABO_B_1    --------------------------------------------------
+lcl|1ABO_A_1    --------------------------------------------------
+lcl|1PHT_A_1    --------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      ANDTLAAAI----------WEREQEALANLPADLAGLPTDTLFLQPVNMV
+lcl|1ABO_B      --------------------------------------------------
+lcl|1ABO_A      --------------------------------------------------
+lcl|1YCS_B      -----QRIIYEVDDPSLPND-----------------------------E
+lcl|1IHD_C      -----TKSN----------YTVG-------------------------KV
+lcl|1IHW_B      --------------------------------------------------
+lcl|1IHW_A      --------------------------------------------------
+lcl|1IHV_B      --------------------------------------------------
+lcl|1IHV_A      --------------------------------------------------
+lcl|1YCS_A      --------------------------------------------------
+lcl|1PHT_A      -------------A------------------------------------
+lcl|1YCS_B_1    -----QRIIYEVDDPSLPND-----------------------------E
+lcl|1YCS_B_2    -----QRIIYEVDDPSLPND-----------------------------E
+lcl|1YCS_B_3    -----QRIIYEVDDPSLPND-----------------------------E
+lcl|1ABO_B_1    --------------------------------------------------
+lcl|1ABO_A_1    --------------------------------------------------
+lcl|1PHT_A_1    -------------A------------------------------------
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      GVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEHGLI---
+lcl|1ABO_B      --------------------------------------------------
+lcl|1ABO_A      --------------------------------------------------
+lcl|1YCS_B      GITALHN------------------------------AVCAGHTEIVKFL
+lcl|1IHD_C      GVE-----------------------------------------------
+lcl|1IHW_B      --------------------------------------------------
+lcl|1IHW_A      --------------------------------------------------
+lcl|1IHV_B      --------------------------------------------------
+lcl|1IHV_A      --------------------------------------------------
+lcl|1YCS_A      -----KS------------------------------VTC----------
+lcl|1PHT_A      --------------------------------------------------
+lcl|1YCS_B_1    GITALHN------------------------------AVCAGHTEIVKFL
+lcl|1YCS_B_2    GITALHN------------------------------AVCAGHTEIVKFL
+lcl|1YCS_B_3    GITALHN------------------------------AVCAGHTEIVKFL
+lcl|1ABO_B_1    --------------------------------------------------
+lcl|1ABO_A_1    --------------------------------------------------
+lcl|1PHT_A_1    --------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      -------------AWQGQIVGWYCTNLTPE--GYAVES----EAHPGSVQ
+lcl|1IHU_A      ----------------------------------M---------------
+lcl|1ABO_B      --------------------------------------------------
+lcl|1ABO_A      --------------------------------------------------
+lcl|1YCS_B      VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
+lcl|1IHD_C      ----------------------------------N---------------
+lcl|1IHW_B      -------R------------------------------------------
+lcl|1IHW_A      -------R------------------------------------------
+lcl|1IHV_B      -------R------------------------------------------
+lcl|1IHV_A      -------R------------------------------------------
+lcl|1YCS_A      -------------TYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMA
+lcl|1PHT_A      --------------------------------------------------
+lcl|1YCS_B_1    VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
+lcl|1YCS_B_2    VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
+lcl|1YCS_B_3    VQFGVNVNAADSDGWTPLHCAASCNNVQVC--KFLVES----GAAVFAMT
+lcl|1ABO_B_1    --------------------------------------------------
+lcl|1ABO_A_1    --------------------------------------------------
+lcl|1PHT_A_1    --------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      -----I--------------------------------------------
+lcl|1IHU_A      -------------------------------------------LMGKGGV
+lcl|1ABO_B      -------------------------------------------LYDFVAS
+lcl|1ABO_A      -------------------------------------------LYDFVAS
+lcl|1YCS_B      YSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGV-IYALWDYEPQ
+lcl|1IHD_C      -------------------------------------------LVNAVPQ
+lcl|1IHW_B      ------------------------------------------DSRDPVWK
+lcl|1IHW_A      ------------------------------------------DSRDPVWK
+lcl|1IHV_B      ------------------------------------------DSRDPVWK
+lcl|1IHV_A      ------------------------------------------DSRDPVWK
+lcl|1YCS_A      -----I--------------------------------------------
+lcl|1PHT_A      ------------------------------------EGYQYRALYDYKKE
+lcl|1YCS_B_1    YSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGV-IYALWDYEPQ
+lcl|1YCS_B_2    YSDMQTAADKCEEMEEGYTQCSQFLYG-----------------------
+lcl|1YCS_B_3    YSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGV-IYALWDYEPQ
+lcl|1ABO_B_1    -------------------------------------------LYDFVAS
+lcl|1ABO_A_1    -------------------------------------------LYDFVAS
+lcl|1PHT_A_1    ------------------------------------EGYQYRALYDYKKE
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      GKTTMAAAIAVRLADMGFD------VHLTTSDP-------AAHLS-MTLN
+lcl|1ABO_B      GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
+lcl|1ABO_A      GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
+lcl|1YCS_B      NDDELPM----KEGDCMTI--------IHREDED-----EIEWWW---AR
+lcl|1IHD_C      -LKDIA----NVKGEQVVN--------IGSQDMN-----DNVWLT---LA
+lcl|1IHW_B      GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
+lcl|1IHW_A      GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
+lcl|1IHV_B      GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
+lcl|1IHV_A      GPAKL-----LWKGEGAVV--------IQDNS-------DIK--------
+lcl|1YCS_A      --------------------------------------------------
+lcl|1PHT_A      REEDIDL----HLGDILTVNKGSLVA-LGFSDGQEARPEEIGWLNGY-NE
+lcl|1YCS_B_1    NDDELPM----KEGDCMTI--------IHREDED-----EIEWWW---AR
+lcl|1YCS_B_2    --------------------------------------------------
+lcl|1YCS_B_3    NDDELPM----KEGDCMTI--------IHREDED-----EIEWWW---AR
+lcl|1ABO_B_1    GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
+lcl|1ABO_A_1    GDNTLS----ITKGEKLRV--------LGYNH-------NGEWCE---AQ
+lcl|1PHT_A_1    REEDIDL----HLGDILTVNKGSLVA-LGFSDGQEARPEEIGWLNGY-NE
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      GSLNNLQVSRIDPHEETERYRQHVLETKGKELDEAGKRLLEEDLRSPCTE
+lcl|1ABO_B      --TK----------------------------------------------
+lcl|1ABO_A      --TK----------------------------------------------
+lcl|1YCS_B      -L-N----------------------------------------------
+lcl|1IHD_C      KKIN----------------------------------------------
+lcl|1IHW_B      --------------------------------------------------
+lcl|1IHW_A      --------------------------------------------------
+lcl|1IHV_B      --------------------------------------------------
+lcl|1IHV_A      --------------------------------------------------
+lcl|1YCS_A      --------------------------------------------------
+lcl|1PHT_A      -T-T----------------------------------------------
+lcl|1YCS_B_1    -L-N----------------------------------------------
+lcl|1YCS_B_2    --------------------------------------------------
+lcl|1YCS_B_3    -L-N----------------------------------------------
+lcl|1ABO_B_1    --TK----------------------------------------------
+lcl|1ABO_A_1    --TK----------------------------------------------
+lcl|1PHT_A_1    -T-T----------------------------------------------
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      EIAVFQAFSRVIREAGKRFVVMDTAPTGHTLLLLDATGAYHREIAKKMGE
+lcl|1ABO_B      --------------------------------------------------
+lcl|1ABO_A      --------------------------------------------------
+lcl|1YCS_B      --------------------------------------------------
+lcl|1IHD_C      -------------TDCDKT-------------------------------
+lcl|1IHW_B      --------------------------------------------------
+lcl|1IHW_A      --------------------------------------------------
+lcl|1IHV_B      --------------------------------------------------
+lcl|1IHV_A      --------------------------------------------------
+lcl|1YCS_A      --------------------------------------------------
+lcl|1PHT_A      --------------------------------------------------
+lcl|1YCS_B_1    --------------------------------------------------
+lcl|1YCS_B_2    --------------------------------------------------
+lcl|1YCS_B_3    --------------------------------------------------
+lcl|1ABO_B_1    --------------------------------------------------
+lcl|1ABO_A_1    --------------------------------------------------
+lcl|1PHT_A_1    --------------------------------------------------
+                                                                  
+
+lcl|1VIE_A      --------------------------------------------------
+lcl|1IHU_A      KGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAGIHPWGW
+lcl|1ABO_B      ---------------------------------------------NGQGW
+lcl|1ABO_A      ---------------------------------------------NGQGW
+lcl|1YCS_B      ---------------------------------------------DKEGY
+lcl|1IHD_C      --------------------------------------------------
+lcl|1IHW_B      -------------------------------------------------V
+lcl|1IHW_A      -------------------------------------------------V
+lcl|1IHV_B      -------------------------------------------------V
+lcl|1IHV_A      -------------------------------------------------V
+lcl|1YCS_A      --------------------------------------------------
+lcl|1PHT_A      ---------------------------------------------GERGD
+lcl|1YCS_B_1    ---------------------------------------------DKEGY
+lcl|1YCS_B_2    --------------------------------------------------
+lcl|1YCS_B_3    ---------------------------------------------DKEGY
+lcl|1ABO_B_1    ---------------------------------------------NGQGW
+lcl|1ABO_A_1    ---------------------------------------------NGQGW
+lcl|1PHT_A_1    ---------------------------------------------GERGD
+                                                                  
+
+lcl|1VIE_A      Y-PVAA-LERI---------------------N-----------
+lcl|1IHU_A      I-INNS-LSIADTRSPLLRMRAQQELPQIESVKR----QHAS--
+lcl|1ABO_B      V-PSNY-ITPV---------------------NS----------
+lcl|1ABO_A      V-PSNY-ITPV---------------------NS----------
+lcl|1YCS_B      V-PRNL-LGLY---------------------PRIKPRQRSL-A
+lcl|1IHD_C      --------------------------------------------
+lcl|1IHW_B      V-PRRKA-KII----------------------RD---------
+lcl|1IHW_A      V-PRRKA-KII----------------------RD---------
+lcl|1IHV_B      V-PRRKA-KII----------------------RD---------
+lcl|1IHV_A      V-PRRKA-KII----------------------RD---------
+lcl|1YCS_A      YKQSQHMTEV----------------------V-----------
+lcl|1PHT_A      F-PGTY-VEYI---------------------GR----KKISPP
+lcl|1YCS_B_1    V-PRNL-LGLY---------------------PRIKPRQRSL-A
+lcl|1YCS_B_2    --------------------------------------------
+lcl|1YCS_B_3    V-PRNL-LGLY---------------------PRIKPRQRSL-A
+lcl|1ABO_B_1    V-PSNY-ITPV---------------------NS----------
+lcl|1ABO_A_1    V-PSNY-ITPV---------------------NS----------
+lcl|1PHT_A_1    F-PGTY-VEYI---------------------GR---------K
+                                                            
+
+
+

nextflow/tests/checks/blast.nf/.checks

@@ -0,0 +1,20 @@
+set -e
+
+#
+# run normal mode
+#
+$NXF_RUN $WITH_DOCKER | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > blast'` == 5 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process > sort'` == 1 ]] || false
+diff .expected .stdout || false
+
+#
+# run resume mode
+#
+$NXF_RUN $WITH_DOCKER -resume | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process > blast'` == 5 ]] || false
+[[ `grep INFO .nextflow.log | grep -c 'Cached process > sort'` == 1 ]] || false
+diff .expected .stdout || false
+

nextflow/tests/checks/blast.nf/.expected

@@ -0,0 +1,34 @@
+1aboA	1ABO:A	100.00	57	0	0	1	57	5	61	2e-40	  120
+1aboA	1ABO:B	100.00	57	0	0	1	57	5	61	2e-40	  120
+1aboA	1IHD:A	36.11	36	21	1	5	40	287	320	0.62	18.1
+1aboA	1IHD:A	75.00	8	2	0	28	35	179	186	0.69	17.7
+1aboA	1IHD:C	36.11	36	21	1	5	40	287	320	0.62	18.1
+1aboA	1IHD:C	75.00	8	2	0	28	35	179	186	0.69	17.7
+1aboA	1YCS:B	25.49	51	36	1	5	53	175	225	3e-04	27.3
+1ihvA	1IHN:A	35.00	20	13	0	25	44	72	91	7.0	14.6
+1ihvA	1IHN:A	66.67	9	3	0	35	43	28	36	3.7	15.4
+1ihvA	1IHN:B	35.00	20	13	0	25	44	72	91	7.0	14.6
+1ihvA	1IHN:B	66.67	9	3	0	35	43	28	36	3.7	15.4
+1ihvA	1IHU:A	27.27	33	24	0	8	40	534	566	5.5	15.0
+1ihvA	1IHV:A	100.00	49	0	0	1	49	4	52	3e-32	99.8
+1ihvA	1IHV:B	100.00	49	0	0	1	49	4	52	3e-32	99.8
+1ihvA	1IHW:A	100.00	49	0	0	1	49	4	52	3e-32	99.8
+1ihvA	1IHW:B	100.00	49	0	0	1	49	4	52	3e-32	99.8
+1ihvA	1YCS:A	54.55	11	5	0	1	11	107	117	0.88	17.3
+1pht	1IHF:B	33.33	21	14	0	53	73	60	80	0.75	18.1
+1pht	1IHS:H	32.00	25	17	0	40	64	175	199	4.0	16.5
+1pht	1IHT:H	32.00	25	17	0	40	64	175	199	4.0	16.5
+1pht	1PHT:A	100.00	80	0	0	1	80	5	84	1e-56	  164
+1pht	1YCS:B	23.08	26	20	0	19	44	115	140	3.4	16.5
+1pht	1YCS:B	30.43	23	16	0	6	28	175	197	0.015	23.5
+1vie	1IHM:A	31.82	22	11	1	19	40	343	360	9.0	14.6
+1vie	1IHM:B	31.82	22	11	1	19	40	343	360	9.0	14.6
+1vie	1IHM:C	31.82	22	11	1	19	40	343	360	9.0	14.6
+1vie	1IHU:A	26.92	26	18	1	25	49	156	181	8.5	14.6
+1vie	1VIE:A	100.00	51	0	0	1	51	12	62	1e-35	  108
+1ycsB	1ABO:A	24.07	54	39	1	3	56	6	57	4e-05	28.5
+1ycsB	1ABO:B	24.07	54	39	1	3	56	6	57	4e-05	28.5
+1ycsB	1IHU:A	35.71	14	9	0	6	19	251	264	6.9	15.4
+1ycsB	1PHT:A	30.43	23	16	0	6	28	10	32	0.013	22.3
+1ycsB	1YCS:B	100.00	60	0	0	1	60	170	229	3e-42	  131
+

nextflow/tests/checks/buffer.nf/.checks

@@ -0,0 +1,21 @@
+set -e
+
+#
+# run normal mode
+#
+$NXF_RUN | tee .stdout
+
+[[ `grep -c 'Submitted process > blastThemAll' .nextflow.log` == 3 ]] || false
+[[ `grep -c 'p1.fa p2.fa' .stdout` == 1 ]] || false
+[[ `grep -c 'p3.fa p4.fa' .stdout` == 1 ]] || false
+[[ `grep -c 'p5.fa' .stdout` == 1 ]] || false
+
+#
+# run resume mode
+#
+$NXF_RUN -resume | tee .stdout
+
+[[ `grep -c 'Cached process > blastThemAll' .nextflow.log` == 3 ]] || false
+[[ `grep -c 'p1.fa p2.fa' .stdout` == 1 ]] || false
+[[ `grep -c 'p3.fa p4.fa' .stdout` == 1 ]] || false
+[[ `grep -c 'p5.fa' .stdout` == 1 ]] || false

nextflow/tests/checks/cache-bak.nf/.checks

@@ -0,0 +1,42 @@
+set -e
+
+# Skip test if AWS keys are missing
+if [[ ! $AWS_ACCESS_KEY_ID ]]; then
+  echo "Skip cache-bak test since AWS keys are not available"
+  exit 0
+fi
+
+#
+# setup env
+#
+export NXF_IGNORE_RESUME_HISTORY=true
+export NXF_UUID=$(uuidgen | tr [:upper:] [:lower:])
+
+#
+# run normal mode
+#
+$NXF_RUN -name test_1 | tee .stdout
+[[ `grep -c 'Submitted process > foo' .nextflow.log` == 1 ]] || false
+
+#
+# backup cache
+#
+NXF_WORK=s3://nextflow-ci/cache-test  \
+  $NXF_CMD -log .nextflow-backup.log plugin nf-tower:cache-backup
+
+#
+# remove it
+#
+rm -rf .nextflow
+
+#
+# restore cache
+#
+NXF_WORK=s3://nextflow-ci/cache-test  \
+  $NXF_CMD -log .nextflow-restore.log plugin nf-tower:cache-restore
+
+#
+# run resume mode
+#
+$NXF_RUN -name test_2 -resume $NXF_UUID | tee .stdout
+[[ `grep -c 'Cached process > foo' .nextflow.log` == 1 ]] || false

nextflow/tests/checks/chunk.nf/.checks

@@ -0,0 +1,15 @@
+set -e
+
+#
+# run normal mode
+#
+$NXF_RUN --chunkSize 3 --input .data.fa | tee .stdout
+
+[[ `grep -c 'Submitted process > foo' .nextflow.log` == 2 ]] || false
+
+#
+# run resume mode
+#
+$NXF_RUN -resume --chunkSize 3 --input .data.fa | tee .stdout
+
+[[ `grep -c 'Cached process > foo' .nextflow.log` == 2 ]] || false

nextflow/tests/checks/chunk.nf/.data.fa

@@ -0,0 +1,14 @@
+>1aboA
+NLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPS
+NYITPVN
+>1ycsB
+KGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGY
+VPRNLLGLYP
+>1pht
+GYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIG
+WLNGYNETTGERGDFPGTYVEYIGRKKISP
+>1vie
+DRVRKKSGAAWQGQIVGWYCTNLTPEGYAVESEAHPGSVQIYPVAALERI
+N
+>1ihvA
+NFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD

nextflow/tests/checks/cli-args.nf/.checks

@@ -0,0 +1,35 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN --alpha uno --beta \* --delta 'x_{1,2}.fasta' --gamma hello\ world --omega '--foo bar' a b c | tee stdout
+
+< stdout grep -F 'alpha: uno'
+< stdout grep -F 'beta : *' 
+< stdout grep -F 'delta: x_{1,2}.fasta' 
+< stdout grep -F 'gamma: hello world' 
+< stdout grep -F 'omega: --foo bar' 
+< stdout grep -F 'args : a_b_c' 
+
+#
+# check quotes
+#
+echo ''
+$NXF_RUN --alpha "a'b" --beta 'a"b' --delta 'x'  --gamma "x" --omega x "a b c" | tee stdout
+
+< stdout grep -F "alpha: a'b"
+< stdout grep -F 'beta : a"b' 
+< stdout grep -F 'delta: x' 
+< stdout grep -F 'gamma: x' 
+< stdout grep -F 'omega: x' 
+< stdout grep -F 'args : a b c' 
+
+#
+# check the log command handle properly quoted filter options 
+#
+$NXF_CMD -log .nextflow.log log last -F 'container = "ubuntu"' | tee log 
+[[ $? == 0 ]] || exit 1
+$NXF_CMD -log .nextflow.log log last -F "container = 'ubuntu'" | tee log
+[[ $? == 0 ]] || exit 1

nextflow/tests/checks/cli-fs.nf/.checks

@@ -0,0 +1,20 @@
+# Skip test if AWS keys are missing
+if [ -z "$AWS_ACCESS_KEY_ID" ]; then
+  echo "Missing AWS credentials -- Skipping test"
+  exit 0
+fi
+
+## random file name
+NAME=test-cmd-$(basename `mktemp`).file
+
+## create random file
+head -c 1000000 </dev/urandom >myfile
+
+## upload it
+$NXF_CMD -log cmd-fs-1.log fs cp myfile s3://nextflow-ci/$NAME
+
+## download it
+$NXF_CMD -log cmd-fs-2.log fs cp s3://nextflow-ci/$NAME $NAME
+
+## check they are equals
+diff myfile $NAME || false

nextflow/tests/checks/collect-file.nf/.checks

@@ -0,0 +1,8 @@
+echo ''
+echo \$ $NXF_RUN
+$NXF_RUN | tee stdout
+
+[[ `<stdout grep -c 'Entries are saved to file'` == 1 ]] || false
+[[ `<stdout grep -c 'alpha'` == 1 ]] || false
+[[ `<stdout grep -c 'beta'` == 1 ]] || false
+[[ `<stdout grep -c 'gamma'` == 1 ]] || false

nextflow/tests/checks/collect-record.nf/.checks

@@ -0,0 +1,34 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+echo \$ $NXF_RUN
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > align'` == 6 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > merge'` == 2 ]] || false
+
+[[ `grep -c 'barcode: alpha' stdout` == 1 ]] || false
+[[ `grep -c 'barcode: gamma' stdout` == 1 ]] || false
+[[ `grep -c 'bam : bam1 bam2 bam3' stdout` == 2 ]] || false
+[[ `grep -c 'bai : bai1 bai2 bai3' stdout` == 2 ]] || false
+[[ `grep -c 'seq_ids' stdout` == 2 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+echo \$ $NXF_RUN -resume
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > align'` == 6 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > merge'` == 2 ]] || false
+
+[[ `grep -c 'barcode: alpha' stdout` == 1 ]] || false
+[[ `grep -c 'barcode: gamma' stdout` == 1 ]] || false
+[[ `grep -c 'bam : bam1 bam2 bam3' stdout` == 2 ]] || false
+[[ `grep -c 'bai : bai1 bai2 bai3' stdout` == 2 ]] || false
+[[ `grep -c 'seq_ids' stdout` == 2 ]] || false

nextflow/tests/checks/collect-tuple.nf/.checks

@@ -0,0 +1,34 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+echo \$ $NXF_RUN
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > algn'` == 6 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > merge'` == 2 ]] || false
+
+[[ `grep -c 'barcode: alpha' stdout` == 1 ]] || false
+[[ `grep -c 'barcode: gamma' stdout` == 1 ]] || false
+[[ `grep -c 'bam : bam1 bam2 bam3' stdout` == 2 ]] || false
+[[ `grep -c 'bai : bai1 bai2 bai3' stdout` == 2 ]] || false
+[[ `grep -c 'seq_ids' stdout` == 2 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+echo \$ $NXF_RUN -resume
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > algn'` == 6 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > merge'` == 2 ]] || false
+
+[[ `grep -c 'barcode: alpha' stdout` == 1 ]] || false
+[[ `grep -c 'barcode: gamma' stdout` == 1 ]] || false
+[[ `grep -c 'bam : bam1 bam2 bam3' stdout` == 2 ]] || false
+[[ `grep -c 'bai : bai1 bai2 bai3' stdout` == 2 ]] || false
+[[ `grep -c 'seq_ids' stdout` == 2 ]] || false

nextflow/tests/checks/complex-names.nf/.checks

@@ -0,0 +1,44 @@
+set -e
+
+#
+# basic run 
+#
+echo ''
+$NXF_RUN > stdout
+[[ `<stdout grep -c 'Hello world!'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > bar'` == 1 ]] || false
+( cd foo; 
+[[ -s f1.fa ]] || false
+[[ -s f2.fa ]] || false
+[[ -s f3.fa ]] || false
+[[ -s hello.txt ]] || false
+[[ -s sample.zip ]] || false
+[[ -s sample.html ]] || false
+[[ -s '01_A(R1).fastq' ]] || false
+[[ -s '01_A(R2).fastq' ]] || false
+[[ -s 'sample_(1 2).vcf' ]] || false
+[[ -s .alpha/hello.txt ]] || false
+)
+
+#
+# resume 
+# 
+rm -rf foo 
+echo ''
+$NXF_RUN -resume > stdout
+[[ `<stdout grep -c 'Hello world!'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > bar'` == 1 ]] || false
+( cd foo; 
+[[ -s f1.fa ]] || false
+[[ -s f2.fa ]] || false
+[[ -s f3.fa ]] || false
+[[ -s hello.txt ]] || false
+[[ -s sample.zip ]] || false
+[[ -s sample.html ]] || false
+[[ -s '01_A(R1).fastq' ]] || false
+[[ -s '01_A(R2).fastq' ]] || false
+[[ -s 'sample_(1 2).vcf' ]] || false
+[[ -s .alpha/hello.txt ]] || false
+)

nextflow/tests/checks/config-labels.nf/.checks

@@ -0,0 +1,39 @@
+# apply labels for profile `test1`
+$NXF_RUN -c ../../config-labels.config -profile test1 | tee stdout
+
+< stdout grep "alpha memry: 20 MB" || false
+< stdout grep "alpha queue: std" || false
+
+< stdout grep "beta memry: 10 MB" || false
+< stdout grep "beta queue: small" || false
+
+< stdout grep "delta memry: 70 MB" || false
+< stdout grep "delta queue: big" || false
+< stdout grep "gamma memry: 70 MB" || false
+< stdout grep "gamma queue: big" || false
+
+# apply labels for profile `test2`
+$NXF_RUN -c ../../config-labels.config -profile test2 | tee stdout
+
+< stdout grep "beta memry: 10 MB" || false
+< stdout grep "beta queue: small" || false
+
+< stdout grep "alpha memry: 70 MB" || false
+< stdout grep "alpha queue: big" || false
+< stdout grep "delta memry: 70 MB" || false
+< stdout grep "delta queue: big" || false
+< stdout grep "gamma memry: 70 MB" || false
+< stdout grep "gamma queue: big" || false
+
+# apply labels for profile `test3`
+$NXF_RUN -c ../../config-labels.config -profile test3 | tee stdout
+
+< stdout grep "beta memry: 50 MB" || false
+< stdout grep "beta queue: all" || false
+< stdout grep "alpha memry: 50 MB" || false
+< stdout grep "alpha queue: all" || false
+< stdout grep "delta memry: 50 MB" || false
+< stdout grep "delta queue: all" || false
+
+< stdout grep "gamma memry: 60 MB" || false
+< stdout grep "gamma queue: foo" || false

nextflow/tests/checks/config-secrets.nf/.checks

@@ -0,0 +1,11 @@
+
+set -e
+
+$NXF_CMD secrets set MY_SECRET hello-world
+
+$NXF_RUN -c ../../config-secrets.config | tee stdout
+
+< .nextflow.log grep "Config file used secrets -- reloading config with secrets provider" || false
+< stdout grep "outputDir: results-hello-world" || false
+
+$NXF_CMD secrets delete MY_SECRET

nextflow/tests/checks/config-vars.nf/.checks

@@ -0,0 +1,20 @@
+#
+# run normal mode 
+#
+$NXF_RUN -c ../../config-vars.config | tee stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
+< stdout grep "foo 1,2" || false
+< stdout grep "bar 3,4" || false
+
+
+#
+# run resume mode 
+#
+$NXF_RUN -c ../../config-vars.config -resume | tee stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
+< stdout grep "foo 1,2" || false
+< stdout grep "bar 3,4" || false
+
+

nextflow/tests/checks/copy-no-follow.nf/.checks

@@ -0,0 +1,21 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process '` == 1 ]] || false
+[[ -f outputDir/testFile.txt ]] || false
+[[ -L outputDir/testFileLink.txt ]] || false
+
+#
+# run resume mode
+#
+rm -rf outputDir
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process '` == 1 ]] || false
+[[ -f outputDir/testFile.txt ]] || false
+[[ -L outputDir/testFileLink.txt ]] || false

nextflow/tests/checks/custom-lib.nf/.checks

@@ -0,0 +1,23 @@
+#
+# check the ability to load custom script/classes in the 
+# local `lib` directory 
+#
+set -e
+
+# copy the test script in this directory 
+cp ${NXF_SCRIPT:-../../custom-lib.nf} test.nf
+
+# crate a library class 
+mkdir -p lib
+cat >lib/Foo.groovy <<EOL
+class Foo {
+
+  static String hello() { "Hello world!" }
+
+}
+EOL
+
+${NXF_CMD:-nextflow} run test.nf | tee stdout
+
+[[ `< stdout grep -c 'Hello world!'` == 1 ]] || false
+

nextflow/tests/checks/demo.nf/.checks

@@ -0,0 +1,32 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+echo \$ $NXF_RUN
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > sayHello'` == 5 ]] || false
+
+[[ `grep 'Hola world!' stdout` ]] || false
+[[ `grep 'Γεια σου world!' stdout` ]] || false
+[[ `grep 'Hello world!' stdout` ]] || false
+[[ `grep 'Bojour world!' stdout` ]] || false
+[[ `grep 'Ciao world!' stdout` ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+echo \$ $NXF_RUN -resume
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > sayHello'` == 5 ]] || false
+
+[[ `grep 'Hola world!' stdout` ]] || false
+[[ `grep 'Γεια σου world!' stdout` ]] || false
+[[ `grep 'Hello world!' stdout` ]] || false
+[[ `grep 'Bojour world!' stdout` ]] || false
+[[ `grep 'Ciao world!' stdout` ]] || false

nextflow/tests/checks/dyn-mem.nf/.big.txt

@@ -0,0 +1,2 @@
+1234567890
+1234567890

nextflow/tests/checks/dyn-mem.nf/.checks

@@ -0,0 +1,18 @@
+set -e
+
+#
+# run normal mode
+#
+$NXF_RUN -process.debug | tee stdout
+
+[[ `< .nextflow.log grep -c 'Submitted process'` == 2 ]] || false
+[[ `< stdout grep 'task=.small.txt mem=100 MB'` ]] || false
+[[ `< stdout grep 'task=.big.txt mem=200 MB'` ]] || false
+
+#
+# run resume mode
+#
+$NXF_RUN -process.debug -resume | tee stdout
+
+[[ `< .nextflow.log grep -c 'Cached process'` == 2 ]] || false
+

nextflow/tests/checks/dyn-mem.nf/.small.txt

@@ -0,0 +1 @@
+12345

nextflow/tests/checks/dynamic-filename-typed.nf/.checks

@@ -0,0 +1,45 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN --input .data.txt | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 4 ]] || false
+
+grep '~ Saving my_delta.txt' stdout
+grep '~ Saving my_omega.txt' stdout
+grep '~ Saving my_gamma.txt' stdout
+grep '~ Saving my_alpha.txt' stdout
+
+test -f my_alpha.txt
+test -f my_delta.txt
+test -f my_gamma.txt
+test -f my_omega.txt
+
+diff my_alpha.txt .expected
+diff my_delta.txt .expected
+diff my_gamma.txt .expected
+diff my_omega.txt .expected
+
+rm my_* 
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN --input .data.txt -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 4 ]] || false
+
+grep '~ Saving my_delta.txt' stdout
+grep '~ Saving my_omega.txt' stdout
+grep '~ Saving my_gamma.txt' stdout
+grep '~ Saving my_alpha.txt' stdout
+
+test -f my_alpha.txt
+test -f my_delta.txt
+test -f my_gamma.txt
+test -f my_omega.txt

nextflow/tests/checks/dynamic-filename-typed.nf/.data.txt

@@ -0,0 +1 @@
+Hello

nextflow/tests/checks/dynamic-filename-typed.nf/.expected

@@ -0,0 +1,2 @@
+Hello
+World

nextflow/tests/checks/dynamic-filename.nf/.checks

@@ -0,0 +1,45 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 4 ]] || false
+
+grep '~ Saving my_delta.txt' stdout
+grep '~ Saving my_omega.txt' stdout
+grep '~ Saving my_gamma.txt' stdout
+grep '~ Saving my_alpha.txt' stdout
+
+test -f my_alpha.txt
+test -f my_delta.txt
+test -f my_gamma.txt
+test -f my_omega.txt
+
+diff my_alpha.txt .expected
+diff my_delta.txt .expected
+diff my_gamma.txt .expected
+diff my_omega.txt .expected
+
+rm my_* 
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 4 ]] || false
+
+grep '~ Saving my_delta.txt' stdout
+grep '~ Saving my_omega.txt' stdout
+grep '~ Saving my_gamma.txt' stdout
+grep '~ Saving my_alpha.txt' stdout
+
+test -f my_alpha.txt
+test -f my_delta.txt
+test -f my_gamma.txt
+test -f my_omega.txt

nextflow/tests/checks/dynamic-filename.nf/.expected

@@ -0,0 +1,2 @@
+Hello
+World

nextflow/tests/checks/dynamic-storedir.nf/.checks

@@ -0,0 +1,76 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 4 ]] || false
+
+grep "Result $PWD/cache/omega/result.txt" stdout
+grep "Result $PWD/cache/delta/result.txt" stdout
+grep "Result $PWD/cache/alpha/result.txt" stdout
+grep "Result $PWD/cache/gamma/result.txt" stdout
+
+test -f my_alpha.txt
+test -f my_delta.txt
+test -f my_gamma.txt
+test -f my_omega.txt
+
+diff my_alpha.txt .expected
+diff my_delta.txt .expected
+diff my_gamma.txt .expected
+diff my_omega.txt .expected
+
+rm my_* 
+
+
+
+#
+# run normal mode -- this time store result are used
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -E -c '\[skipping\] Stored process > foo'` == 4 ]] || false
+
+grep "Result $PWD/cache/omega/result.txt" stdout
+grep "Result $PWD/cache/delta/result.txt" stdout
+grep "Result $PWD/cache/alpha/result.txt" stdout
+grep "Result $PWD/cache/gamma/result.txt" stdout
+
+test -f my_alpha.txt
+test -f my_delta.txt
+test -f my_gamma.txt
+test -f my_omega.txt
+
+diff my_alpha.txt .expected
+diff my_delta.txt .expected
+diff my_gamma.txt .expected
+diff my_omega.txt .expected
+
+rm my_* 
+
+#
+# run resume mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -E -c '\[skipping\] Stored process > foo'` == 4 ]] || false
+
+grep "Result $PWD/cache/omega/result.txt" stdout
+grep "Result $PWD/cache/delta/result.txt" stdout
+grep "Result $PWD/cache/alpha/result.txt" stdout
+grep "Result $PWD/cache/gamma/result.txt" stdout
+
+test -f my_alpha.txt
+test -f my_delta.txt
+test -f my_gamma.txt
+test -f my_omega.txt
+
+diff my_alpha.txt .expected
+diff my_delta.txt .expected
+diff my_gamma.txt .expected
+diff my_omega.txt .expected

nextflow/tests/checks/dynamic-storedir.nf/.expected

@@ -0,0 +1,2 @@
+Hello
+World

nextflow/tests/checks/each-file.nf/.checks

@@ -0,0 +1,35 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo (p1.fa)'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo (p2.fa)'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo (p3.fa)'` == 1 ]] || false
+
+[[ `< stdout grep -c '>1ycsB'` == 2 ]] || false
+[[ `< stdout grep -c '>1pht'` == 2 ]]  || false
+[[ `< stdout grep -c '>1aboA'` == 1 ]] || false
+[[ `< stdout grep -c '>1ihvA'` == 1 ]] || false
+[[ `< stdout grep -c '>1vie'` == 1 ]]  || false
+
+
+
+#
+# run resume mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo (p1.fa)'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo (p2.fa)'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo (p3.fa)'` == 1 ]] || false
+
+[[ `< stdout grep -c '>1ycsB'` == 2 ]] || false
+[[ `< stdout grep -c '>1pht'` == 2 ]]  || false
+[[ `< stdout grep -c '>1aboA'` == 1 ]] || false
+[[ `< stdout grep -c '>1ihvA'` == 1 ]] || false
+[[ `< stdout grep -c '>1vie'` == 1 ]]  || false

nextflow/tests/checks/env-container-with(special)chars.nf/.checks

@@ -0,0 +1,78 @@
+set -e
+export NXF_ANSI_LOG=false
+
+#
+# create the `hello.sh` executable script
+#
+mkdir -p bin
+echo "echo Hola mundo" > bin/hello.sh
+chmod +x bin/hello.sh
+
+#
+# create the nextflow config file 
+#
+cat << EOF > nextflow.config
+env.FOO = 'HOLA'
+process.container = 'quay.io/nextflow/bash'
+EOF
+
+#
+# create the nextflow script 
+#
+cat << EOF > foo.nf
+process foo {
+  debug true
+  input: 
+  env 'BAR'
+  script:
+  '''
+  env | grep -E "^(FOO|BAR)" | sort
+  hello.sh
+  '''
+}
+
+workflow {
+  channel.value('Hello World!') | foo
+}
+EOF
+
+#
+# not the testing part 
+#
+
+# NF plain run  
+$NXF_CMD run foo.nf | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+# NF run with trace
+$NXF_CMD run foo.nf -with-trace | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+# NF run with docker
+$NXF_CMD run foo.nf -with-docker | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+
+# NF run with docker and trace
+$NXF_CMD run foo.nf -with-trace -with-docker | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false

nextflow/tests/checks/env-container.nf/.checks

@@ -0,0 +1,78 @@
+set -e
+export NXF_ANSI_LOG=false
+
+#
+# create the `hello.sh` executable script
+#
+mkdir -p bin
+echo "echo Hola mundo" > bin/hello.sh
+chmod +x bin/hello.sh
+
+#
+# create the nextflow config file 
+#
+cat << EOF > nextflow.config
+env.FOO = 'HOLA'
+process.container = 'quay.io/nextflow/bash'
+EOF
+
+#
+# create the nextflow script 
+#
+cat << EOF > foo.nf
+process foo {
+  debug true
+  input: 
+  env 'BAR'
+  script:
+  '''
+  env | grep -E "^(FOO|BAR)" | sort
+  hello.sh
+  '''
+}
+
+workflow {
+  channel.value('Hello World!') | foo
+}
+EOF
+
+#
+# not the testing part 
+#
+
+# NF plain run  
+$NXF_CMD run foo.nf | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+# NF run with trace
+$NXF_CMD run foo.nf -with-trace | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+# NF run with docker
+$NXF_CMD run foo.nf -with-docker | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false
+
+
+# NF run with docker and trace
+$NXF_CMD run foo.nf -with-trace -with-docker | tee stdout
+
+# run tests 
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c 'FOO=HOLA'` == 1 ]] || false
+[[ `< stdout grep -c 'BAR=Hello World!'` == 1 ]] || false
+[[ `< stdout grep -c 'Hola mundo'` == 1 ]] || false

nextflow/tests/checks/env-typed.nf/.checks

@@ -0,0 +1,17 @@
+#
+# run normal mode 
+#
+$NXF_RUN | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
+[[ `< .stdout grep 'bar says Hello'` ]] || false
+
+
+#
+# run resume mode 
+#
+$NXF_RUN -resume | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
+[[ `< .stdout grep 'bar says Hello'` ]] || false
+

nextflow/tests/checks/env.nf/.checks

@@ -0,0 +1,17 @@
+#
+# run normal mode 
+#
+$NXF_RUN | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 2 ]] || false
+[[ `< .stdout grep 'bar says Hello'` ]] || false
+
+
+#
+# run resume mode 
+#
+$NXF_RUN -resume | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 2 ]] || false
+[[ `< .stdout grep 'bar says Hello'` ]] || false
+

nextflow/tests/checks/error-finish.nf/.checks

@@ -0,0 +1,21 @@
+set -e
+export NXF_ASSETS=$PWD/assets
+
+#
+# First run test `success` is `true` 
+#
+set +e
+echo ''
+$NXF_RUN > stdout
+status=$?
+set -e
+# the exit status must NOT be zero because the pipeline throws an error
+[ $status -ne 0 ] || false
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 3 ]] || false
+
+[[ `grep -c 'success: false' stdout` == 1 ]] || false
+[[ `grep -c 'exitStatus: 99' stdout` == 1 ]] || false
+
+[[ `grep -c 'run_1' stdout` == 1 ]] || false
+[[ `grep -c 'run_2' stdout` == 1 ]] || false

nextflow/tests/checks/error-ignore-then-fail.nf/.checks

@@ -0,0 +1,13 @@
+set -e
+
+set +e
+echo ''
+$NXF_CMD -q run $NXF_SCRIPT -c .config  > stdout
+status=$?
+set -e
+
+[ $status -ne 0 ] || false
+
+[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 3 ]] || false
+[[ `< .nextflow.log grep -c 'Submitted process > bar'` == 1 ]] || false
+[[ `< .nextflow.log grep -c 'Error is ignored'` == 1 ]] || false

nextflow/tests/checks/error-ignore-then-fail.nf/.config

@@ -0,0 +1,6 @@
+workflow {
+    failOnIgnore = true
+}
+process {
+  errorStrategy = 'ignore'
+}

nextflow/tests/checks/error-message.nf/.checks

@@ -0,0 +1,11 @@
+set +e
+$NXF_RUN | tee stdout
+set -e
+
+if [[ "$NXF_SYNTAX_PARSER" == "v2" ]] ; then
+    # strict parser should give compile-time error
+    < stdout grep "error-message.nf:19:1: \`printx\` is not defined"
+else
+    # legacy parser should give runtime error
+    < stdout grep "Check script '.*error-message.nf' at line: 19"
+fi

nextflow/tests/checks/error.nf/.checks

@@ -0,0 +1,23 @@
+set -e
+
+#
+# run normal mode
+#
+$NXF_RUN -c .config | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task1'` == 3 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task2'` == 3 ]] || false
+
+[[ `grep 'NOTE' .nextflow.log | grep -E -c "Process .* terminated with an error exit status"` == 3 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -c .config -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > task1'` == 3 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > task2'` == 3 ]] || false
+
+[[ `grep 'NOTE' .nextflow.log | grep -E -c "Process .* terminated with an error exit status"` == 3 ]] || false

nextflow/tests/checks/error.nf/.config

@@ -0,0 +1 @@
+process.errorStrategy = { task.exitStatus >= 1 ? 'retry' : 'ignore' }

nextflow/tests/checks/escape-globs.nf/.checks

@@ -0,0 +1,24 @@
+set -e
+
+mkdir \[work-dir\]
+
+#
+# run normal mode 
+#
+$NXF_RUN -w \[work-dir\] | tee stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< stdout grep -c -F 'match: file[a-b].txt'` == 1 ]] || false
+[[ `< stdout grep -c -F 'match: file-*.txt'` == 1 ]] || false
+[[ `< stdout grep -c -F 'match: file-?.txt'` == 1 ]] || false
+
+#
+# run resume mode 
+#
+$NXF_RUN -w \[work-dir\] -resume | tee stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false
+[[ `< stdout grep -c -F 'match: file[a-b].txt'` == 1 ]] || false
+[[ `< stdout grep -c -F 'match: file-*.txt'` == 1 ]] || false
+[[ `< stdout grep -c -F 'match: file-?.txt'` == 1 ]] || false
+

nextflow/tests/checks/eval-out-typed.nf/.checks

@@ -0,0 +1,17 @@
+#
+# run normal mode 
+#
+$NXF_RUN | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< .stdout grep 'GNU bash'` ]] || false
+
+
+#
+# run resume mode 
+#
+$NXF_RUN -resume | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false
+[[ `< .stdout grep 'GNU bash'` ]] || false
+

nextflow/tests/checks/eval-out.nf/.checks

@@ -0,0 +1,17 @@
+#
+# run normal mode 
+#
+$NXF_RUN | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+[[ `< .stdout grep 'GNU bash'` ]] || false
+
+
+#
+# run resume mode 
+#
+$NXF_RUN -resume | tee .stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false
+[[ `< .stdout grep 'GNU bash'` ]] || false
+

nextflow/tests/checks/exit-if-empty.nf/.checks

@@ -0,0 +1,10 @@
+set +e
+set -o pipefail
+
+echo ''
+echo \$ $NXF_RUN
+$NXF_RUN | tee stdout
+
+# must return a non-zero exit status 
+[[ $? == 0 ]] && exit 1
+[[ `<stdout grep -c 'Channel empty terminating'` == 1 ]] || false

nextflow/tests/checks/exitstatus-fail.nf/.checks

@@ -0,0 +1,18 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN 
+[[ $? == 0 ]] && exit 1
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume 
+[[ $? == 0 ]] && exit 1
+
+exit 0

nextflow/tests/checks/fair.nf/.checks

@@ -0,0 +1,21 @@
+set -e
+export NXF_ANSI_LOG=false
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 26 ]] || false
+cmp stdout .expected || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 26 ]] || false
+cmp stdout .expected || false

nextflow/tests/checks/fair.nf/.expected

@@ -0,0 +1,26 @@
+[1, a]
+[2, b]
+[3, c]
+[4, d]
+[5, e]
+[6, f]
+[7, g]
+[8, h]
+[9, i]
+[10, j]
+[11, k]
+[12, l]
+[13, m]
+[14, n]
+[15, o]
+[16, p]
+[17, q]
+[18, r]
+[19, s]
+[20, t]
+[21, u]
+[22, v]
+[23, w]
+[24, x]
+[25, y]
+[26, z]

nextflow/tests/checks/file-with-blanks.nf/.checks

@@ -0,0 +1,20 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
+[[ `< stdout grep -c 'Hello' ` == 1 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false
+[[ `< stdout grep -c 'Hello' ` == 1 ]] || false

nextflow/tests/checks/file-with-quote.nf/.checks

@@ -0,0 +1,20 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
+[[ `< stdout grep -c 'Hello' ` == 1 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false
+[[ `< stdout grep -c 'Hello' ` == 1 ]] || false

nextflow/tests/checks/files.nf/.checks

@@ -0,0 +1,25 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+echo \$ $NXF_RUN
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > split'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > printTwo'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > printLast'` == 2 ]] || false
+
+
+
+#
+# RESUME mode
+#
+echo ''
+echo \$ $NXF_RUN -resume
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > split'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > printTwo'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > printLast'` == 2 ]] || false

nextflow/tests/checks/fusion-symlink.nf/.checks

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+# Skip test if AWS keys are missing
+if [ -z "$AWS_ACCESS_KEY_ID" ]; then 
+  echo "Missing AWS credentials -- Skipping test"
+  exit 0
+fi
+
+OUTDIR="s3://nextflow-ci/work/ci-test/fusion-symlink/$(uuidgen)"
+
+#
+# normal run
+#
+echo initial run
+$NXF_RUN -c .config --outdir "$OUTDIR"
+
+$NXF_CMD fs cp "$OUTDIR/data.txt" data.txt
+cmp data.txt .expected || false
+
+#
+# resume run
+#
+echo resumed run
+$NXF_RUN -c .config --outdir "$OUTDIR" -resume
+
+$NXF_CMD fs cp "$OUTDIR/data.txt" data.txt
+cmp data.txt .expected || false

nextflow/tests/checks/fusion-symlink.nf/.config

@@ -0,0 +1,5 @@
+workDir = 's3://nextflow-ci/work'
+fusion.enabled = true
+fusion.exportStorageCredentials = true
+wave.enabled = true
+docker.runOptions = '-e FUSION_TRACING_DESTINATION=objectstore://'

nextflow/tests/checks/fusion-symlink.nf/.expected

@@ -0,0 +1 @@
+HELLO

nextflow/tests/checks/glob.nf/.checks

@@ -0,0 +1,27 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > recurseDir'` == 1 ]] || false
+
+grep 'result1: file2.fa' stdout
+grep 'result1: file3.fa' stdout
+grep 'result1: file4.fa' stdout
+grep 'result2: file5.txt' stdout
+
+#
+# run resume mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > recurseDir'` == 1 ]] || false
+
+grep 'result1: file2.fa' stdout
+grep 'result1: file3.fa' stdout
+grep 'result1: file4.fa' stdout
+grep 'result2: file5.txt' stdout

nextflow/tests/checks/hello.nf/.checks

@@ -0,0 +1,31 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > sayhello'` == 1 ]] || false
+[[ `grep -c 'Hello world!' stdout` == 1 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > sayhello'` == 1 ]] || false
+[[ `grep -c 'Hello world!' stdout` == 1 ]] || false
+
+#
+# checks reports 
+#
+echo ''
+$NXF_RUN -with-report -with-timeline -with-trace -with-dag | tee stdout
+
+[ -s report-*.html ] || false
+[ -s timeline-*.html ] || false
+[ -s trace-*.txt ] || false
+[ -s dag-*.html ] || false

nextflow/tests/checks/input.nf/.checks

@@ -0,0 +1,28 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 2 ]] || false
+
+[[ `grep -c '1 - a' stdout` == 1 ]] || false
+[[ `grep -c '1 - b' stdout` == 1 ]] || false
+[[ `grep -c 'foo out: a' stdout` == 1 ]] || false
+[[ `grep -c 'foo out: b' stdout` == 1 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 2 ]] || false
+
+[[ `grep -c '1 - a' stdout` == 1 ]] || false
+[[ `grep -c '1 - b' stdout` == 1 ]] || false
+[[ `grep -c 'foo out: a' stdout` == 1 ]] || false
+[[ `grep -c 'foo out: b' stdout` == 1 ]] || false

nextflow/tests/checks/mixing-langs.nf/.checks

@@ -0,0 +1,21 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > perlTask'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > pyTask'` == 1 ]] || false
+
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > perlTask'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > pyTask'` == 1 ]] || false

nextflow/tests/checks/mixing-langs.nf/.expected

@@ -0,0 +1 @@
+avg: 43.5159945284 - 36.8211561596

nextflow/tests/checks/nativeCode.nf/.checks

@@ -0,0 +1,20 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > nativeCode'` == 1 ]] || false
+grep 'Hello world' stdout
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > nativeCode'` == 1 ]] || false
+grep 'Hello world' stdout

nextflow/tests/checks/nullable-path.nf/.checks

@@ -0,0 +1,18 @@
+set +e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee .stdout
+[[ $? == 0 ]] || false
+cmp .expected .stdout || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee .stdout
+[[ $? == 0 ]] || false
+cmp .expected .stdout || false

nextflow/tests/checks/nullable-path.nf/.expected

@@ -0,0 +1,2 @@
+empty input
+

nextflow/tests/checks/opt-file.nf/.checks

@@ -0,0 +1,18 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `< .nextflow.log grep -c 'Cached process > foo'` == 1 ]] || false

nextflow/tests/checks/output-dsl.nf/.checks

@@ -0,0 +1,102 @@
+
+echo "Initial run"
+$NXF_RUN --save_bam_bai | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
+sed "s|"$(dirname "$(realpath "$0")")"||g" stdout > stdout.norm
+cmp .expected-text stdout.norm || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ -f results/align/sample1.bai ]] || false
+[[ -f results/align/sample1.bam ]] || false
+[[ -f results/align/sample2.bai ]] || false
+[[ -f results/align/sample2.bam ]] || false
+[[ -f results/align/sample3.bai ]] || false
+[[ -f results/align/sample3.bam ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false
+
+
+echo "Run again with overwrite enabled and JSON output"
+$NXF_RUN -output-format json --save_bam_bai | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Submitted process > quant') == 3 ]] || false
+sed "s|"$(dirname "$(realpath "$0")")"||g" stdout > stdout.norm
+cmp .expected-json stdout.norm || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ -f results/align/sample1.bai ]] || false
+[[ -f results/align/sample1.bam ]] || false
+[[ -f results/align/sample2.bai ]] || false
+[[ -f results/align/sample2.bam ]] || false
+[[ -f results/align/sample3.bai ]] || false
+[[ -f results/align/sample3.bam ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false
+
+
+echo "Run with some outputs disabled"
+rm -rf results
+
+$NXF_RUN -resume | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > quant') == 3 ]] || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ ! -e results/align ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false
+
+
+echo "Resumed run"
+rm -rf results
+
+$NXF_RUN --save_bam_bai -resume | tee stdout
+
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > fastqc') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > align') == 3 ]] || false
+[[ $(grep INFO .nextflow.log | grep -c 'Cached process > quant') == 3 ]] || false
+
+[[ -f results/log/sample1.fastqc.log ]] || false
+[[ -f results/log/sample2.fastqc.log ]] || false
+[[ -f results/log/sample3.fastqc.log ]] || false
+[[ -f results/align/sample1.bai ]] || false
+[[ -f results/align/sample1.bam ]] || false
+[[ -f results/align/sample2.bai ]] || false
+[[ -f results/align/sample2.bam ]] || false
+[[ -f results/align/sample3.bai ]] || false
+[[ -f results/align/sample3.bam ]] || false
+[[ -L results/quant/sample1 ]] || false
+[[ -L results/quant/sample2 ]] || false
+[[ -L results/quant/sample3 ]] || false
+[[ -f results/samples.csv ]] || false
+[[ -f results/summary_report.html ]] || false
+[[ -f results/summary_data/data.json ]] || false
+[[ -f results/summary_data/fastqc.txt ]] || false

nextflow/tests/checks/output-dsl.nf/.expected-json

@@ -0,0 +1,8 @@
+{
+    "samples": "/results/samples.csv",
+    "summary": {
+        "report": "/results/summary_report.html",
+        "data": "/results/summary_data/data.json",
+        "fastqc": "/results/summary_data/fastqc.txt"
+    }
+}

nextflow/tests/checks/output-dsl.nf/.expected-text

@@ -0,0 +1,11 @@
+
+Outputs:
+
+  /results
+
+  samples: samples.csv
+
+  summary:
+    report: summary_report.html
+    data: summary_data/data.json
+    fastqc: summary_data/fastqc.txt

nextflow/tests/checks/output-file.nf/.checks

@@ -0,0 +1,25 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
+
+[[ `< stdout grep 'dummy'` ]] || false
+
+
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
+
+[[ `< stdout grep 'dummy'` ]] || false
+

nextflow/tests/checks/output-globs.nf/.checks

@@ -0,0 +1,28 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > bar'` == 1 ]] || false
+
+[[ `< stdout grep -E 'foo.*/a/a/2\.txt' ` ]] || false
+[[ `< stdout grep -E 'bar.*/a/a/2\.txt' ` ]] || false
+
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > bar'` == 1 ]] || false
+
+[[ `< stdout grep -E 'foo.*/a/a/2\.txt' ` ]] || false
+[[ `< stdout grep -E 'bar.*/a/a/2\.txt' ` ]] || false
+

nextflow/tests/checks/output-links.nf/.checks

@@ -0,0 +1,18 @@
+set -e
+
+#
+# run normal mode 
+#
+$NXF_RUN -process.scratch true | tee stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Submitted process'` == 1 ]] || false
+
+
+
+#
+# run resume mode 
+#
+$NXF_RUN -resume -process.scratch true | tee stdout
+
+[[ `grep INFO .nextflow.log | grep -c 'Cached process'` == 1 ]] || false
+

nextflow/tests/checks/output-val.nf/.checks

@@ -0,0 +1,30 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+$NXF_RUN | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > foo'` == 1 ]] || false
+
+[[ `< stdout grep 'x: 100'` ]] 				|| false
+[[ `< stdout grep 'y: two hundred'` ]] 		|| false
+[[ `< stdout grep 'str: Hello'` ]] 			|| false
+[[ `< stdout grep 'exp: prot-100.out'` ]] 	|| false
+
+
+
+#
+# RESUME mode
+#
+echo ''
+$NXF_RUN -resume | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Cached process > foo'` == 1 ]] || false
+
+[[ `< stdout grep 'x: 100'` ]] 				|| false
+[[ `< stdout grep 'y: two hundred'` ]] 		|| false
+[[ `< stdout grep 'str: Hello'` ]] 			|| false
+[[ `< stdout grep 'exp: prot-100.out'` ]] 	|| false
+

nextflow/tests/checks/params-dsl.nf/.checks

@@ -0,0 +1,48 @@
+
+echo "Test successful run"
+echo
+$NXF_RUN --input ./data > stdout
+
+< stdout grep -F 'params.input = [./data]'
+< stdout grep -F 'params.save_intermeds = false'
+< stdout grep -F 'params.method = auto'
+
+echo
+echo "Test missing required param"
+echo
+set +e
+$NXF_RUN &> stdout ; ret=$?
+set -e
+
+[[ $ret != 0 ]] || false
+
+< stdout grep -F 'Parameter `input` is required'
+
+echo
+echo "Test overwrite script param from command line"
+echo
+$NXF_RUN -c ../../params-dsl.config --input 'alpha,beta' --save_intermeds --method special > stdout
+
+< stdout grep -F 'params.input = [alpha, beta]'
+< stdout grep -F 'params.save_intermeds = true'
+< stdout grep -F 'params.method = special'
+
+echo
+echo "Test overwrite script param from config profile"
+echo
+$NXF_RUN -c ../../params-dsl.config -profile test > stdout
+
+< stdout grep -F 'params.input = [alpha, beta, delta]'
+< stdout grep -F 'params.save_intermeds = true'
+< stdout grep -F 'params.method = special'
+
+echo
+echo "Test invalid param"
+echo
+set +e
+$NXF_RUN --inputs ./data &> stdout ; ret=$?
+set -e
+
+[[ $ret != 0 ]] || false
+
+< stdout grep -F 'Parameter `inputs` was specified'

nextflow/tests/checks/plugin-registry.nf/.checks

@@ -0,0 +1,14 @@
+set -e
+
+#
+# run normal mode
+#
+echo ''
+NXF_PLUGINS_REGISTRY_URL=https://plugin-registry.dev-tower.net/api NXF_PLUGINS_DIR=$PWD/.nextflow/plugins/ $NXF_RUN -plugins nf-ci-integration-test@0.1.0 | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Downloading plugin nf-ci-integration-test@0.1.0'` == 1 ]] || false
+[[ `grep -c 'Pipeline is starting using nf-ci-test-integration plugin' stdout` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > sayhello'` == 1 ]] || false
+[[ `grep -c 'Hello world!' stdout` == 1 ]] || false
+[[ `grep -c 'Pipeline completed using nf-ci-test-integration plugin' stdout` == 1 ]] || false
+