From a5265513001fdbcea14388670fdfabe5ae2367f6 Mon Sep 17 00:00:00 2001
From: FelixKrueger <felix.krueger@babraham.ac.uk>
Date: Thu, 19 Mar 2020 18:13:15 +0000
Subject: [PATCH] Added Bowtie2 module and test workflow

---
 tools/bowtie2/main.nf              | 55 ++++++++++++++++++++++++++++++
 tools/bowtie2/meta.yml             | 37 ++++++++++++++++++++
 tools/bowtie2/test/main.nf         | 31 +++++++++++++++++
 tools/bowtie2/test/nextflow.config |  2 ++
 4 files changed, 125 insertions(+)
 create mode 100644 tools/bowtie2/main.nf
 create mode 100644 tools/bowtie2/meta.yml
 create mode 100755 tools/bowtie2/test/main.nf
 create mode 100644 tools/bowtie2/test/nextflow.config

diff --git a/tools/bowtie2/main.nf b/tools/bowtie2/main.nf
new file mode 100644
index 00000000..e5ebf47f
--- /dev/null
+++ b/tools/bowtie2/main.nf
@@ -0,0 +1,55 @@
+nextflow.preview.dsl=2
+params.genome = ''
+
+process BOWTIE2 {
+	// depending on the genome used one might want/need to adjust the memory settings.
+	// For the E. coli test data this is probably not required
+
+	// label 'bigMem' 
+	// label 'multiCore'
+		
+    input:
+	    tuple val(name), path(reads)
+		val (outdir)
+		val (bowtie2_args)
+		val (verbose)
+
+	output:
+	    path "*bam",  emit: bam
+		path "*stats.txt", emit: stats 
+
+	publishDir "$outdir/bowtie2",
+		mode: "copy", overwrite: true
+
+	script:
+		if (verbose){
+			println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
+		}
+
+		cores = 4
+
+		readString = ""
+
+		// Options we add are
+		bowtie2_options = bowtie2_args
+		bowtie2_options +=  " --no-unal "  // We don't need unaligned reads in the BAM file
+		
+		// single-end / paired-end distinction. Might also be handled via params.single_end 
+		if (reads instanceof List) {
+			readString = "-1 " + reads[0] + " -2 " + reads[1]
+		}
+		else {
+			readString = "-U " + reads
+		}
+		
+		index = params.genome["bowtie2"]
+		bowtie2_name = name + "_" + params.genome["name"]
+
+		println ("bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString}  2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam")
+		"""
+		module load bowtie2
+		module load samtools
+		bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString}  2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
+		"""
+
+}
diff --git a/tools/bowtie2/meta.yml b/tools/bowtie2/meta.yml
new file mode 100644
index 00000000..b3b31a94
--- /dev/null
+++ b/tools/bowtie2/meta.yml
@@ -0,0 +1,37 @@
+name: Bowtie 2 
+description: Ultrafast alignment to reference genome
+keywords:
+    - Alignment
+    - Short reads
+    - FM Index
+tools:
+    - fastqc:
+        description: |
+            Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
+            to long reference sequences. It is particularly good at aligning reads of about
+            50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively
+            long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep
+            its memory footprint small: for the human genome, its memory footprint is typically
+            around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
+        homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+        documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
+input:
+    -
+        - sample_id:
+            type: string
+            description: Sample identifier
+        - reads:
+            type: file
+            description: Input FastQ file, or pair of files
+output:
+    -
+        - report:
+            type: file
+            description: mapping statistics report
+            pattern: *bowtie2_stats.txt
+        - alignment:
+            type: file
+            description: alignment file in BAM format
+            pattern: *bowtie2.bam
+authors:
+    - @FelixKrueger
diff --git a/tools/bowtie2/test/main.nf b/tools/bowtie2/test/main.nf
new file mode 100755
index 00000000..5c02914b
--- /dev/null
+++ b/tools/bowtie2/test/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl=2
+
+params.outdir = "."
+params.genome = ""
+params.bowtie2_args = ''
+// Bowtie2 arguments should be supplied in the following format to work:
+// --bowtie2_args="--score-min L,0,-0.8"
+
+params.verbose = false
+
+if (params.verbose){
+    println ("[WORKFLOW] BOWTIE2 ARGS: "      + params.bowtie2_args)
+}
+
+// for other genomes this needs to be handled somehow to return all possible genomes
+genomeValues = ["name" : params.genome]
+genomeValues["bowtie2"] = "/bi/home/fkrueger/VersionControl/nf-core-modules/test-datasets/indices/bowtie2/E_coli/${params.genome}";
+
+include '../main.nf'   params(genome: genomeValues)
+
+ch_read_files = Channel
+  .fromFilePairs('../../../test-datasets/Ecoli*{1,2}.fastq.gz',size:-1)
+  // .view()  // to check whether the input channel works
+
+workflow {
+
+    main:
+        BOWTIE2(ch_read_files, params.outdir, params.bowtie2_args, params.verbose)
+    
+}
\ No newline at end of file
diff --git a/tools/bowtie2/test/nextflow.config b/tools/bowtie2/test/nextflow.config
new file mode 100644
index 00000000..c137a138
--- /dev/null
+++ b/tools/bowtie2/test/nextflow.config
@@ -0,0 +1,2 @@
+docker.enabled = true
+params.outdir = './results'