adding run seqtk pipeline

Author: elowy01

FASTQ/FASTQ_QA/run_seqtk_pipeline/run_seqtk_qa.nf

@@ -0,0 +1,109 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Pipeline to run SEQTK QA
+ * 
+ *  @author
+ * Ernesto Lowy <ernesto.lowy@gmail.com>
+*/
+
+// Define defaults
+def defaults = [
+    min_length: 70
+]
+
+
+// params defaults
+params.help = false
+params.min_length = defaults.min_length
+
+//print usage
+if (params.help) {
+    log.info ''
+    log.info 'Pipeline to run FASTQA on a FASTQ file'
+    log.info '---------------------------------'
+    log.info 'FASTQA is based on  SEQTK .'
+    log.info ''
+    log.info 'Usage: '
+    log.info '    nextflow run_seqtk_qa.nf --pwd $DB_PASS --output_dir ./out --dbname elowy_hgdp_03102018 --runs runs.txt'
+    log.info ''
+    log.info 'Options:'
+    log.info '	--help	                    Show this message and exit.'
+    log.info '	--pwd PWD	            Password for connecting the ReseqTrack DB.'
+    log.info '	--dbname DBNAME	            ReseqTrack DB name.'
+    log.info '	--host HOSTNAME	            Hostname of the MySQL ReseqTrack DB.'
+    log.info '	--user USER		    Username of the MySQL ReseqTrack DB.'
+    log.info '	--port PORT		    Port number of the MySQL ReseqTrack DB.'
+    log.info '	--min_length MIN_LENGTH     Minimum sequence length.'
+    log.info '	--program PROGRAM	    Path to seqtk binary.'
+    log.info '	--reseqtrack RESEQTRACK     Path to the reseqtrack repository.'
+    log.info '	--queue QUEUE               Name of the queue to use on the LSF (eg, production-rh74, research-rh74).'
+    log.info '	--output_dir OUTPUT_DIR     Directory that will contain the output files.'
+    log.info '	--runs RUN_FILE	            File containing runs to be analyzed'
+    log.info '	       The format of RUN_FILE is:'
+    log.info '	       name'
+    log.info '	       ERR0001'
+    log.info '	       ERR0002'
+    log.info '	       ERR0003' 
+    log.info ''
+    exit 1
+}
+
+ /*
+  * Validate input file
+  */
+  run_file = file(params.runs)
+  if( !run_file.exists() ) exit 1, "Missing file with run ids: ${run_file}"
+
+ /*
+  * Create a channel for different run ids
+  */
+Channel
+    .fromPath(run_file)
+    .splitCsv(header:true)
+    .map{ row-> row.name }
+    .set { runs_ch }
+
+process runFastqSimpleQA {
+        /*
+	Process to run perl fastq_simple_qa_by_seqtk.pl on the FASTQs in a RESEQTRACK DB
+        */
+
+	memory '2 GB'
+        executor 'lsf'
+        queue params.queue
+        cpus 1
+
+	input:
+	val x from runs_ch
+
+	output:
+	file out_fastqa
+	val x into run_id
+
+	script:
+        """
+	perl ${params.reseqtrack}/scripts/qc/fastq_simple_qa_by_seqtk.pl -dbhost ${params.host} -dbname ${params.dbname} -dbuser ${params.user} \
+	-dbpass ${params.pwd} -dbport ${params.port} -run_id $x -collection_type FASTQ -new_collection_type FQ_OK -min_length ${params.min_length} \
+	-output_dir ${params.output_dir} -program ${params.program} -clobber 1> out_fastqa 
+        """
+}
+
+process moveFinalFile {
+	/*
+	Process to move the final output file to the output folder set in params.output_dir
+	*/
+	publishDir "${params.output_dir}", saveAs:{ filename -> "$filename" }
+
+	input:
+        val run_id
+	file out_fastqa
+
+	output:
+	file "${run_id}.seqtk.out"
+	
+	script:
+	"""
+	mv ${out_fastqa} ${run_id}.seqtk.out
+	"""
+}