Added Docker image script. Added docker support to pipeline.

Dockerfile

@@ -0,0 +1,106 @@
+FROM openjdk:8
+
+LABEL authors="[email protected],[email protected]" \
+    description="Docker image containing all requirements for NGI-MethylSeq pipeline"
+
+# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        g++ \
+        gcc \
+        gfortran \
+        libbz2-dev \
+        libcurl4-openssl-dev \
+        libgsl0-dev \
+        liblzma-dev \
+        libncurses5-dev \
+        libpcre3-dev \
+        libreadline-dev \
+        libssl-dev \
+        make \
+        python-dev \
+        zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install pip
+RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
+    python /opt/get-pip.py && \
+    rm /opt/get-pip.py
+
+RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \
+    unzip /opt/fastqc_v0.11.5.zip -d /opt/ && \
+    chmod 755 /opt/FastQC/fastqc && \
+    ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
+    rm /opt/fastqc_v0.11.5.zip
+
+# Install cutadapt
+RUN pip install cutadapt
+
+# Install TrimGalore
+RUN mkdir /opt/TrimGalore && \
+    curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v0.4.2.zip -o /opt/TrimGalore/trim_galore_v0.4.2.zip && \
+    unzip /opt/TrimGalore/trim_galore_v0.4.2.zip -d /opt/TrimGalore && \
+    ln -s /opt/TrimGalore/trim_galore /usr/local/bin/trim_galore && \
+    rm /opt/TrimGalore/trim_galore_v0.4.2.zip
+
+# Install SAMTools
+RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 -o /opt/samtools-1.3.1.tar.bz2 && \
+    tar xvjf /opt/samtools-1.3.1.tar.bz2 -C /opt/ && \
+    cd /opt/samtools-1.3.1 && \
+    make && \
+    make install && \
+    rm /opt/samtools-1.3.1.tar.bz2
+
+# Install PicardTools
+RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/picard-tools-2.0.1.zip -o /opt/picard-tools-2.0.1.zip && \
+    unzip /opt/picard-tools-2.0.1.zip -d /opt/ && \
+    rm /opt/picard-tools-2.0.1.zip
+ENV PICARD_HOME /opt/picard-tools-2.0.1
+
+# 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 && \
+    rm /opt/Bismark/bismark.zip
+
+# Install Qualimap
+RUN mkdir /opt/Qualimap && \
+    curl -fsSL https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip -o /opt/Qualimap/qualimap.zip && \
+    unzip /opt/Qualimap/qualimap.zip -d /opt/Qualimap && \
+    ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
+    rm /opt/Qualimap/qualimap.zip
+
+# Install BWA
+RUN mkdir /opt/bwa && \
+    curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2 -o /opt/bwa/bwa.tar.bz2 && \
+    tar xvjf /opt/bwa/bwa.tar.bz2 -C /opt/bwa/ && \
+    cd /opt/bwa/bwa-0.7.15/ && \
+    make && \
+    ln -s /opt/bwa/bwa-0.7.15/bwa /usr/local/bin/bwa && \
+    rm /opt/bwa/bwa.tar.bz2
+
+# Install bwa-meth
+RUN pip install toolshed && \
+    pip install git+git://github.com/brentp/bwa-meth.git
+
+# Install MethylDackel
+RUN mkdir /opt/MethylDackel && \
+    curl -fsSL https://github.com/dpryan79/MethylDackel/archive/0.2.1.zip -o /opt/MethylDackel/MethylDackel.zip && \
+    unzip /opt/MethylDackel/MethylDackel.zip -d /opt/MethylDackel && \
+    cd /opt/MethylDackel/MethylDackel-0.2.1 && \
+    make && \
+    make install prefix=/usr/local/bin && \
+    rm /opt/MethylDackel/MethylDackel.zip
+
+# Install MultiQC
+RUN pip install git+git://github.com/ewels/MultiQC.git

conf/docker.config

@@ -0,0 +1,23 @@
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * -------------------------------------------------
+ *  Nextflow config file for use with Docker
+ * -------------------------------------------------
+ * Defines basic usage limits and docker image id.
+ * Imported under the default 'docker' Nextflow
+ * profile in nextflow.config
+ * NOTE: Not suitable for production use, assumes
+ * compute limits of only 16GB memory and 1 CPU core.
+ */
+
+docker {
+  enabled = true
+}
+
+process {
+  container = 'scilifelab/ngi-methylseq'
+  cpus = 1
+  memory = 16.GB
+  time = 48.h
+}

conf/testing.config

@@ -0,0 +1,30 @@
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * --------------------------------------------------------
+ *  Nextflow config file for automated testing with Travis
+ * --------------------------------------------------------
+ */
+
+params {
+  // Need to specify this here (as well as main.nf) so that timeline and trace work below.
+  outdir = './results'
+}
+
+docker {
+  enabled = true
+}
+process {
+  container = 'scilifelab/ngi-methylseq'
+  cpus = 2
+  memory = 7.GB
+  time = 48.h
+}
+timeline {
+  enabled = true
+  file = "${params.outdir}/NGI-MethylSeq_timeline.html"
+}
+trace {
+  enabled = true
+  file = "${params.outdir}/NGI-MethylSeq_trace.txt"
+}

conf/uppmax-devel.config

@@ -1,9 +1,13 @@
-/* -------------------------------------------------
- *  Example Nextflow config file for UPPMAX (milou)
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
  * -------------------------------------------------
- * Defines reference genomes, using iGenome paths
- * Should be saved either with Nextflow installation or
- * as file ~/.nextflow/config
+ *  Nextflow config file for UPPMAX (milou / irma)
+ * -------------------------------------------------
+ * Differs from main UPPMAX config in that it submits
+ * jobs to the `devcore` queue, which has much faster
+ * queue times. All jobs are limited to 1 hour to be eligible
+ * for this queue.
  */
 
 
@@ -93,8 +97,8 @@ process {
     cpus = { 4 * task.attempt }
     memory = { 32.GB * task.attempt }
   }
-  $pileOMeth {
-    module = ['bioinfo-tools', 'PileOMeth']
+  $methyldackel {
+    module = ['bioinfo-tools', 'MethylDackel']
     cpus = { 6 * task.attempt }
     memory = { 48.GB * task.attempt }
   }

conf/uppmax.config

@@ -1,9 +1,12 @@
-/* -------------------------------------------------
- *  Example Nextflow config file for UPPMAX (milou)
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * -------------------------------------------------
+ *  Nextflow config file for UPPMAX (milou / irma)
  * -------------------------------------------------
  * Defines reference genomes, using iGenome paths
- * Should be saved either with Nextflow installation or
- * as file ~/.nextflow/config
+ * Imported under the default 'standard' Nextflow
+ * profile in nextflow.config
  */
 
 
@@ -99,8 +102,8 @@ process {
     cpus = { 4 * task.attempt }
     memory = { 32.GB * task.attempt }
   }
-  $pileOMeth {
-    module = ['bioinfo-tools', 'PileOMeth']
+  $methyldackel {
+    module = ['bioinfo-tools', 'MethylDackel']
     cpus = { 6 * task.attempt }
     memory = { 48.GB * task.attempt }
   }

nextflow.config

@@ -18,11 +18,14 @@ profiles {
   devel {
     includeConfig 'conf/uppmax-devel.config'
   }
-
-  // UNDER DEVELOPMENT (not yet written)
   docker {
-    process.container = 'your/image'
-    docker.enabled = true
+    includeConfig 'conf/docker.config'
+  }
+  testing {
+    includeConfig 'conf/testing.config'
+  }
+  none {
+    // Don't load any config (for use with custom home configs)
   }
 
 }