Initial commit

tools/fastq_screen/main.nf

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+nextflow.preview.dsl=2
+
+process FASTQ_SCREEN {
+	
+	// depending on the number of genomes and the type of genome (e.g. plants!), memory needs to be ample!
+	// label 'bigMem'
+	// label 'multiCore'
+
+    input:
+	    tuple val(name), path(reads)
+		val (outputdir)
+		val (fastq_screen_args)
+		val (verbose)
+
+	output:
+	    path "*png",  emit: png
+	    path "*html", emit: html
+		path "*txt",  emit: report
+
+	publishDir "$outputdir",
+		mode: "link", overwrite: true
+
+    script:
+		fastq_screen_args = fastq_screen_args.replaceAll(/'/,"")
+
+		if (verbose){
+			println ("[MODULE] FASTQ SCREEN ARGS: "+ fastq_screen_args)
+		}
+
+	"""
+	module load fastq_screen
+	fastq_screen $fastq_screen_args $reads
+	"""
+
+}

tools/fastq_screen/meta.yml

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+name: FastQ Screen
+description: Run FastQ Screen on sequenced reads
+keywords:
+    - Quality Control
+    - Species Screen
+    - Contamination
+tools:
+    - fastqc:
+        description: |
+            FastQC gives general quality metrics about your reads.
+            It provides information about the quality score distribution
+            across your reads, the per base sequence content (%A/C/G/T).
+            You get information about adapter contamination and other
+            overrepresented sequences.
+        homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
+        documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html
+input:
+    -
+        - sample_id:
+            type: string
+            description: Sample identifier
+        - reads:
+            type: file
+            description: Input FastQ file
+output:
+    -
+        - report:
+            type: file
+            description: FastQC report
+            pattern: *_fastqc.{zip,html}
+authors:
+    - @felix