Merge pull request #28 from FelixKrueger/trim_galore

Added functional Trim Galore module

tools/trim_galore/main.nf

@@ -1,35 +1,101 @@
-process trim_galore {
-    tag "$sample_id"
-    publishDir "${params.outdir}/trim_galore", mode: 'copy',
-        saveAs: {filename ->
-            if (filename.indexOf("_fastqc") > 0) "FastQC/$filename"
-            else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
-            else filename
-        }
+nextflow.preview.dsl=2
 
-    container 'quay.io/biocontainers/trim-galore:0.6.5--0'
+params.singlecell = ''
+params.rrbs       = ''
+params.pbat       = ''
+params.single_end  = false
 
-    input:
-    tuple sample_id, path(reads)
+params.trim_nextseq = 0
 
-    output:
-    tuple name, path("*fq.gz")
-    path "*trimming_report.txt"
-    path "*_fastqc.{zip,html}"
+params.clip_r1 = 0
+params.clip_r2 = 0
+params.three_prime_clip_r1 = 0
+params.three_prime_clip_r2 = 0
+
+
+process TRIM_GALORE {	
+    
+    // container 'quay.io/biocontainers/trim-galore:0.6.5--0' // maybe later
+    // tag "$sample_id"
+
+	input:
+	    tuple val (name), path (reads)
+		val (outdir)
+		val (trim_galore_args)
+		val (verbose)
+
+	output:
+	    tuple val(name), path ("*fq.gz"),             emit: reads
+		path "*trimming_report.txt", optional: true,  emit: report
+		
+        // Trimming reports are not generated for e.g. --hardtrim5, --clock etc
+        // saveAs: {filename ->
+        //   else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
+        //   else filename
+        // }
+
+	publishDir "${outdir}/trim_galore",
+		mode: "copy", overwrite: true
 
     script:
-    c_r1 = clip_r1 > 0 ? "--clip_r1 ${clip_r1}" : ''
-    c_r2 = clip_r2 > 0 ? "--clip_r2 ${clip_r2}" : ''
-    tpc_r1 = three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${three_prime_clip_r1}" : ''
-    tpc_r2 = three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${three_prime_clip_r2}" : ''
-    nextseq = params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : ''
-    if (params.singleEnd) {
-        """
-        trim_galore --fastqc --gzip $c_r1 $tpc_r1 $nextseq $reads
-        """
-    } else {
-        """
-        trim_galore --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq $reads
-        """
-    }
+		if (verbose){
+			println ("[MODULE] TRIM GALORE ARGS: " + trim_galore_args)
+		}
+		
+        trim_galore_args += " --gzip "           // we like small files
+
+		pairedString = 0
+		if (reads instanceof List) {
+			pairedString = 1
+            trim_galore_args += " --paired "
+		}
+		
+        if (params.clip_r1 > 0){
+            trim_galore_args += " --clip_r1 ${params.clip_r1} "
+        }
+        if (params.clip_r2 > 0){
+            trim_galore_args += " --clip_r2 ${params.clip_r2} "
+        }
+        if (params.three_prime_clip_r1> 0){
+            trim_galore_args += " --three_prime_clip_r1 ${params.three_prime_clip_r1} "
+        }
+        if (params.three_prime_clip_r2 > 0){
+            trim_galore_args += " --three_prime_clip_r2 ${params.three_prime_clip_r2} "
+        }
+        
+        if (params.trim_nextseq > 0){
+            trim_galore_args += " --nextseq ${params.trim_nextseq} "
+        }   
+    
+        
+        // Pre-set parameters for certain bisulfite-seq applications
+        if (params.singlecell){
+            trim_galore_args += " --clip_r1 6 "
+            if (pairedString == 1){
+                trim_galore_args += " --clip_r2 6 "
+            }
+        }
+        if (params.rrbs){
+            trim_galore_args += " --rrbs "
+        } 
+        if  (params.pbat){
+            trim_galore_args += " --clip_r1 $params.pbat "
+            if (pairedString == 1){
+                trim_galore_args += " --clip_r2 $params.pbat "
+            }
+        }
+
+		"""
+		module load trim_galore
+		trim_galore $trim_galore_args $reads
+		"""
+
 }
+
+
+
+ 
+
+
+  
+

tools/trim_galore/meta.yml

@@ -34,10 +34,8 @@ output:
             type: file
             description: Trim Galore! trimming report
             pattern: *trimming_report.txt
-    -
-        - fastqc_report:
-            type: file
-            description: FastQC report
-            pattern: *_fastqc.{zip,html}
+
 authors:
-    - @ewels
+    - 
+        - @ewels
+        - @FelixKrueger

tools/trim_galore/test/main.nf

@@ -1,13 +1,27 @@
 #!/usr/bin/env nextflow
-echo true
+nextflow.preview.dsl=2
 
-cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
+params.outdir = "."             // gets set in the nextflow.config files (to './results/trim_galore')
+params.verbose = false
+params.trim_galore_args = ''
+// trim_galore_args are best passed into the workflow in the following manner, e.g.:
+// --trim_galore_args="--clip_r1 10 --clip_r2 15 -j 2"
+
+if (params.verbose){
+    println ("[WORKFLOW] TRIM GALORE ARGS: "      + params.trim_galore_args)
+}
+
+// TODO: check the output files in some way
+// include '../../../nf-core/module_testing/check_process_outputs.nf'
+include '../main.nf'  // params (clip_r1: 6, clip_r2: 10) // how to pass additional parameters
+
+ch_read_files = Channel
+  .fromFilePairs('../../../test-datasets/test*{1,2}.fastq.gz',size:-1)
+  // .view()  // to check whether the input channel works
+
+workflow {
+
+    main:
+        TRIM_GALORE (ch_read_files, params.outdir, params.trim_galore_args, params.verbose)
 
-process sayHello {
-  input:
-    val x from cheers
-  script:
-    """
-    echo '$x world!'
-    """
 }

tools/trim_galore/test/nextflow.config

@@ -0,0 +1,2 @@
+// docker.enabled = true
+params.outdir = './results'