Added automated tests. Bugfixing.

.gitignore

@@ -2,4 +2,5 @@
 work/
 data/
 results/
+tests/test_data
 .DS_Store

.travis.yaml

@@ -0,0 +1,21 @@
+sudo: required
+
+language: java
+
+jdk: openjdk8
+
+services:
+  - docker
+install:
+  - mkdir /tmp/nextflow
+  - cd /tmp/nextflow
+  - wget -qO- get.nextflow.io | bash
+  - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+  - cd ${TRAVIS_BUILD_DIR}/tests/
+  - mkdir results
+
+env:
+  - TEST_SUITE=docker_test
+  - TEST_SUITE=docker_test_bwameth
+
+script: "./${TEST_SUITE}.sh"

Dockerfile

@@ -17,6 +17,7 @@ RUN apt-get update && \
         libpcre3-dev \
         libreadline-dev \
         libssl-dev \
+        libtbb-dev \
         make \
         python-dev \
         zlib1g-dev \
@@ -57,20 +58,20 @@ RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/
     rm /opt/picard-tools-2.0.1.zip
 ENV PICARD_HOME /opt/picard-tools-2.0.1
 
+# Install Bowtie2
+RUN mkdir /opt/bowtie2 && \
+    curl -fsSL https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.2/bowtie2-2.3.2-source.zip -o /opt/bowtie2/bowtie2.zip && \
+    unzip /opt/bowtie2/bowtie2.zip -d /opt/bowtie2 && \
+    cd /opt/bowtie2/bowtie2-2.3.2/ && \
+    make && \
+    ln -s /opt/bowtie2/bowtie2-2.3.2/bowtie2 /usr/local/bin/bowtie2 && \
+    rm /opt/bowtie2/bowtie2.zip
+
 # Install Bismark
 RUN mkdir /opt/Bismark && \
     curl -fsSL https://github.com/FelixKrueger/Bismark/archive/0.17.0.zip -o /opt/Bismark/bismark.zip && \
     unzip /opt/Bismark/bismark.zip -d /opt/Bismark && \
-    ln -s /opt/Bismark/Bismark-0.17.0/bam2nuc /usr/local/bin/bam2nuc && \
-    ln -s /opt/Bismark/Bismark-0.17.0/bismark /usr/local/bin/bismark && \
-    ln -s /opt/Bismark/Bismark-0.17.0/bismark2bedGraph /usr/local/bin/bismark2bedGraph && \
-    ln -s /opt/Bismark/Bismark-0.17.0/bismark2report /usr/local/bin/bismark2report && \
-    ln -s /opt/Bismark/Bismark-0.17.0/bismark2summary /usr/local/bin/bismark2summary && \
-    ln -s /opt/Bismark/Bismark-0.17.0/bismark_genome_preparation /usr/local/bin/bismark_genome_preparation && \
-    ln -s /opt/Bismark/Bismark-0.17.0/bismark_methylation_extractor /usr/local/bin/bismark_methylation_extractor && \
-    ln -s /opt/Bismark/Bismark-0.17.0/coverage2cytosine /usr/local/bin/coverage2cytosine && \
-    ln -s /opt/Bismark/Bismark-0.17.0/deduplicate_bismark /usr/local/bin/deduplicate_bismark && \
-    ln -s /opt/Bismark/Bismark-0.17.0/filter_non_conversion /usr/local/bin/filter_non_conversion && \
+    echo "export PATH=/opt/Bismark/Bismark-0.17.0:$PATH" >> ~/.bashrc && \
     rm /opt/Bismark/bismark.zip
 
 # Install Qualimap

assets/summary_email.html

@@ -6,7 +6,7 @@
 
 <img src="data:image/png;base64,<% out << new File("${projectDir}/assets/NGI-MethylSeq_logo.png").bytes.encodeBase64().toString() %>">
 
-<h1>NGI-MethylSeq: RNA-Seq Best Practice v${version}</h1>
+<h1>NGI-MethylSeq: Bisulfite-Seq Best Practice v${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (success){

bismark.nf

@@ -31,6 +31,8 @@ params.reads = "data/*_R{1,2}.fastq.gz"
 params.outdir = './results'
 params.notrim = false
 params.nodedup = false
+params.unmapped = false
+params.non_directional = false
 params.relaxMismatches = false
 params.numMismatches = 0.6
 // 0.6 will allow a penalty of bp * -0.6
@@ -102,6 +104,8 @@ summary['Output dir']     = params.outdir
 summary['Script dir']     = workflow.projectDir
 // log.info "---------------------------------------------------"
 summary['Deduplication']  = params.nodedup ? 'No' : 'Yes'
+summary['Save Unmapped']  = params.unmapped ? 'No' : 'Yes'
+summary['Directional Mode'] = params.non_directional ? 'Yes' : 'No'
 if(params.rrbs) summary['RRBS Mode'] = 'On'
 if(params.relaxMismatches) summary['Mismatch Func'] = 'L,0,-${params.numMismatches} (Bismark default = L,0,-0.2)'
 // log.info "---------------------------------------------------"
@@ -366,7 +370,7 @@ process qualimap {
     file bam from bam_dedup_qualimap
 
     output:
-    file '${bam.baseName}_qualimap' into qualimap_results
+    file "${bam.baseName}_qualimap" into qualimap_results
 
     script:
     gcref = params.genome == 'GRCh37' ? '-gd HUMAN' : ''
@@ -392,7 +396,6 @@ process multiqc {
 
     input:
     file (fastqc:'fastqc/*') from fastqc_results.collect()
-    file ('fastqc/*') from fastqc_results.collect()
     file ('trimgalore/*') from trimgalore_results.collect()
     file ('bismark/*') from bismark_align_log_3.collect()
     file ('bismark/*') from bismark_dedup_log_3.collect()

tests/docker_test.sh

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+
+script_path="../bismark.nf"
+if [ -z $1]
+then
+    echo "No argument given, going to try to run ../bismark.nf"
+else
+    script_path=$1
+fi
+
+data_path="/tmp"
+if [ -d "./test_data" ]
+then
+    data_path="./test_data"
+    echo "Found data directory in current working directory, using ./test_data/"
+fi
+
+curl --version >/dev/null 2>&1 || { echo >&2 "I require curl, but it's not installed. Aborting."; exit 1; }
+tar --version >/dev/null 2>&1 || { echo >&2 "I require tar, but it's not installed. Aborting."; exit 1; }
+docker -v >/dev/null 2>&1 || { echo >&2 "I require docker, but it's not installed. Visit https://www.docker.com/products/overview#/install_the_platform  ."; exit 1; }
+nextflow -v >/dev/null 2>&1 || { echo >&2 "I require nextflow, but it's not installed. If you hava Java, run 'curl -fsSL get.nextflow.io | bash'. If not, install Java."; exit 1; }
+
+data_dir=${data_path}/ngi-bisulfite_test_set
+if [ -d $data_dir ]
+then
+    echo "Found existing test set, using $data_dir"
+else
+    echo "Downloading test set..."
+    curl https://export.uppmax.uu.se/b2013064/test-data/ngi-bisulfite_test_set.tar.bz2 > ${data_path}/ngi-bisulfite_test_set.tar.bz2
+    echo "Unpacking test set..."
+    tar xvjf ${data_path}/ngi-bisulfite_test_set.tar.bz2 -C ${data_path}
+    echo "Done"
+fi
+
+cmd="nextflow run $script_path -resume -profile testing --bismark_index ${data_dir}/references/BismarkIndex/ --reads \"${data_dir}/*.fastq.gz\""
+echo "Starting nextflow... Command:"
+echo $cmd
+echo "-----"
+eval $cmd
+

tests/docker_test_bwameth.sh

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+
+script_path="../bwa-meth.nf"
+if [ -z $1]
+then
+    echo "No argument given, going to try to run ../bwa-meth.nf"
+else
+    script_path=$1
+fi
+
+data_path="/tmp"
+if [ -d "./test_data" ]
+then
+    data_path="./test_data"
+    echo "Found data directory in current working directory, using ./test_data/"
+fi
+
+curl --version >/dev/null 2>&1 || { echo >&2 "I require curl, but it's not installed. Aborting."; exit 1; }
+tar --version >/dev/null 2>&1 || { echo >&2 "I require tar, but it's not installed. Aborting."; exit 1; }
+docker -v >/dev/null 2>&1 || { echo >&2 "I require docker, but it's not installed. Visit https://www.docker.com/products/overview#/install_the_platform  ."; exit 1; }
+nextflow -v >/dev/null 2>&1 || { echo >&2 "I require nextflow, but it's not installed. If you hava Java, run 'curl -fsSL get.nextflow.io | bash'. If not, install Java."; exit 1; }
+
+data_dir=${data_path}/ngi-bisulfite_test_set
+if [ -d $data_dir ]
+then
+    echo "Found existing test set, using $data_dir"
+else
+    echo "Downloading test set..."
+    curl https://export.uppmax.uu.se/b2013064/test-data/ngi-bisulfite_test_set.tar.bz2 > ${data_path}/ngi-bisulfite_test_set.tar.bz2
+    echo "Unpacking test set..."
+    tar xvjf ${data_path}/ngi-bisulfite_test_set.tar.bz2 -C ${data_path}
+    echo "Done"
+fi
+
+cmd="nextflow run $script_path -resume --fasta ${data_dir}/references/WholeGenomeFasta/genome.fa --fasta_index ${data_dir}/references/WholeGenomeFasta/genome.fa.fai --reads \"${data_dir}/*.fastq.gz\""
+echo "Starting nextflow... Command:"
+echo $cmd
+echo "-----"
+eval $cmd
+