TMP_DIR for picard. Unixify main.nf EOL

workflow/main.nf

-/*
- * Copyright (c) 2016. The University of Texas Southwestern Medical Center
- *
- *   This file is part of the BioHPC Workflow Platform
- *
- * Example ChIP-Seq analysis script, demonstrating the BioHPC Workflow Platform
- *
- * @authors
- * David Trudgian <David.Trudgian@UTSouthwestern.edu>
- *
- */
-
-// Path to an input file, or a pattern for multiple inputs
-// Note - $baseDir is the location of this workflow file main.nf
-params.fastq = "$baseDir/../test_data/*.fastq"
-// Path to the BWA Index (.fa file) that we are using for the analysis
-params.index = "/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa"
-
-// First, get the list of fastqs. When multiple files are selected on the web
-// a glob pattern will be passed in
-fastqs = Channel.fromPath( params.fastq )
-// Now find the path to the BWA index directory
-index_path = file(params.index).parent
-// And get the name of the actual index inside that directory
-index_name = file(params.index).name
-
-// bwa_aln
-// Run BWA aln on a fastq file, to produce sai output
-//
-// Input   - fastq_file is taken from the fastq channel
-//         - BWA index at $index_path/$index_name
-//
-// Output  - pair of fastq & generated sai file into the alignments channel 
-process bwa_aln {
-
-    // Tell Nextflow we will use 32 cpus here for BWA
-    cpus 32
-
-    input:
-    file fastq_file from fastqs
-     
-    output:
-    set file(fastq_file), file("${fastq_file.name}.sai") into alignments
-
- 
-    """
-    module load BWA/0.7.5
-    bwa aln $index_path/$index_name -t 32 $fastq_file > "${fastq_file.name}.sai"
-    """
-}
-
-// bwa_aln
-// Run bwa samse to produce sam.gz from an sai alignment
-//
-// Input   - pair of fastq file and corresponding sai file, from alignments channel
-//
-// Output  - .sam.gz into the samfiles channel, and baseDir/output
-process bwa_samse {
-
-    // bwa samse will use a single cpu core
-    cpus 1
-
-    // Publish the outputs we create here into the workflow output directory
-    publishDir "$baseDir/output", mode: 'copy'
-    
-    input:
-    set file(fastq_file), file(sai_file) from alignments 
-
-    output:
-    file "${fastq_file.name}.sam.gz" into samfiles
- 
-    """
-    module load BWA/0.7.5
-    bwa samse -r "@RG\tID:${fastq_file.name}\tLB:${fastq_file.name}\tSM:${fastq_file.name}\tPL:ILLUMINA" $index_path/$index_name\
-    $sai_file $fastq_file | gzip > "${fastq_file.name}.sam.gz"
-    """
-}
-
-// sam2bam
-// Convert SAM file to BAM file, sorting by co-ordinate and indexing
-//
-// Input   - a sam file, (possibly gzipped) from the samfile channel
-//
-// Output  - .sam.gz into the samfiles channel, and baseDir/output
-process sam2bam {
-
-
-    // Tell Nextflow picard will only use one cpu.
-    // We are allocating 32GB to java though, so tell
-    // Nextflow so it can assign the task appropriately.
-    cpus 1
-    memory '32GB'
-
-    // Publish the outputs we create here into the workflow output directory
-    publishDir "$baseDir/output", mode: 'copy'
-    
-    input:
-    file sam_file from samfiles
-
-    output:
-    file "${sam_file.name}.bam" into bamfiles
- 
-    """
-    module add picard/1.127
-    java -Xmx32G -jar \$PICARD/picard.jar SortSam \
-    INPUT="${sam_file}" \
-    OUTPUT="${sam_file.name}.bam" \
-    SORT_ORDER=coordinate \
-    VALIDATION_STRINGENCY=LENIENT \
-    CREATE_INDEX=true
-    """
-}
-
-// macs
-// Peak calling on a bam using MACS 1.4
-//
-// Input   - a bam file, from the bamfiles channel
-//
-// Output  - various wig and bed into baseDir/output 
-process macs14 {
-
-    // Publish the outputs we create here into the workflow output directory
-    publishDir "$baseDir/output", mode: 'copy'
-    
-    input:
-    file bam_file from bamfiles
-
-    output:
-    file "${bam_file}_bwa_nomodel_MACS_wiggle"
-    file "${bam_file}_bwa_nomodel_peaks.bed"
-    file "${bam_file}_bwa_nomodel_peaks.xls"
-    file "${bam_file}_bwa_nomodel_summits.bed"
- 
-    """
-    module add macs/1.4.2
-    macs14 -t ${bam_file} \
-      --name ${bam_file}_bwa_nomodel \
-      --nomodel \
-      --wig \
-      --single-profile \
-      -f BAM
-    """
-}
\ No newline at end of file
+/*
+ * Copyright (c) 2016. The University of Texas Southwestern Medical Center
+ *
+ *   This file is part of the BioHPC Workflow Platform
+ *
+ * Example ChIP-Seq analysis script, demonstrating the BioHPC Workflow Platform
+ *
+ * @authors
+ * David Trudgian <David.Trudgian@UTSouthwestern.edu>
+ *
+ */
+
+// Path to an input file, or a pattern for multiple inputs
+// Note - $baseDir is the location of this workflow file main.nf
+params.fastq = "$baseDir/../test_data/*.fastq"
+// Path to the BWA Index (.fa file) that we are using for the analysis
+params.index = "/project/apps_database/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa"
+
+// First, get the list of fastqs. When multiple files are selected on the web
+// a glob pattern will be passed in
+fastqs = Channel.fromPath( params.fastq )
+// Now find the path to the BWA index directory
+index_path = file(params.index).parent
+// And get the name of the actual index inside that directory
+index_name = file(params.index).name
+
+// bwa_aln
+// Run BWA aln on a fastq file, to produce sai output
+//
+// Input   - fastq_file is taken from the fastq channel
+//         - BWA index at $index_path/$index_name
+//
+// Output  - pair of fastq & generated sai file into the alignments channel 
+process bwa_aln {
+
+    // Tell Nextflow we will use 32 cpus here for BWA
+    cpus 32
+
+    input:
+    file fastq_file from fastqs
+     
+    output:
+    set file(fastq_file), file("${fastq_file.name}.sai") into alignments
+
+ 
+    """
+    module load BWA/0.7.5
+    bwa aln $index_path/$index_name -t 32 $fastq_file > "${fastq_file.name}.sai"
+    """
+}
+
+// bwa_aln
+// Run bwa samse to produce sam.gz from an sai alignment
+//
+// Input   - pair of fastq file and corresponding sai file, from alignments channel
+//
+// Output  - .sam.gz into the samfiles channel, and baseDir/output
+process bwa_samse {
+
+    // bwa samse will use a single cpu core
+    cpus 1
+
+    // Publish the outputs we create here into the workflow output directory
+    publishDir "$baseDir/output", mode: 'copy'
+    
+    input:
+    set file(fastq_file), file(sai_file) from alignments 
+
+    output:
+    file "${fastq_file.name}.sam.gz" into samfiles
+ 
+    """
+    module load BWA/0.7.5
+    bwa samse -r "@RG\tID:${fastq_file.name}\tLB:${fastq_file.name}\tSM:${fastq_file.name}\tPL:ILLUMINA" $index_path/$index_name\
+    $sai_file $fastq_file | gzip > "${fastq_file.name}.sam.gz"
+    """
+}
+
+// sam2bam
+// Convert SAM file to BAM file, sorting by co-ordinate and indexing
+//
+// Input   - a sam file, (possibly gzipped) from the samfile channel
+//
+// Output  - .sam.gz into the samfiles channel, and baseDir/output
+process sam2bam {
+
+
+    // Tell Nextflow picard will only use one cpu.
+    // We are allocating 32GB to java though, so tell
+    // Nextflow so it can assign the task appropriately.
+    cpus 1
+    memory '32GB'
+
+    // Publish the outputs we create here into the workflow output directory
+    publishDir "$baseDir/output", mode: 'copy'
+    
+    input:
+    file sam_file from samfiles
+
+    output:
+    file "${sam_file.name}.bam" into bamfiles
+ 
+    """
+    module add picard/1.127
+    java -Xmx32G -jar \$PICARD/picard.jar SortSam \
+    INPUT="${sam_file}" \
+    OUTPUT="${sam_file.name}.bam" \
+    SORT_ORDER=coordinate \
+    VALIDATION_STRINGENCY=LENIENT \
+    CREATE_INDEX=true \
+    TMP_DIR="${workflow.workDir}/tmp"
+    """
+}
+
+// macs
+// Peak calling on a bam using MACS 1.4
+//
+// Input   - a bam file, from the bamfiles channel
+//
+// Output  - various wig and bed into baseDir/output 
+process macs14 {
+
+    // Publish the outputs we create here into the workflow output directory
+    publishDir "$baseDir/output", mode: 'copy'
+    
+    input:
+    file bam_file from bamfiles
+
+    output:
+    file "${bam_file}_bwa_nomodel_MACS_wiggle"
+    file "${bam_file}_bwa_nomodel_peaks.bed"
+    file "${bam_file}_bwa_nomodel_peaks.xls"
+    file "${bam_file}_bwa_nomodel_summits.bed"
+ 
+    """
+    module add macs/1.4.2
+    macs14 -t ${bam_file} \
+      --name ${bam_file}_bwa_nomodel \
+      --nomodel \
+      --wig \
+      --single-profile \
+      -f BAM
+    """
+}