Merge pull request #2 from ikmb/devel

Triggering release

Author: marchoeppner

bin/report.rb

@@ -110,18 +110,29 @@
 	# 1 ranked B*35:08:01 (abundance: 50.20%) 
 
 	lines = IO.readlines(hisat)
+	header = lines.shift.split("\t")
 
-	lines.each do |l|
+	info = lines.shift.split("\t")
 
-		if line.include?("1 ranked") or line.include?("2 ranked")
 
-			hla_call = line.strip.split(" ")[2]
-			hla_gene = hla_call.split("*")[0]
-			
-			next unless alleles.has_key?(hla_gene)
-
-			alleles[hla_gene]["Hisat"] << hla_gene
+	header.each_with_index do |h,i|
+		if h.include?("EM: A")
+			tmp = info[i]
+			tmp.split(",").each do |t|
+				alleles["A"]["Hisat"] << t.split(" ")[0]
+			end
+		elsif h.include?("EM: B")
+			tmp = info[i]
+                        tmp.split(",").each do |t|
+                                alleles["B"]["Hisat"] << t.split(" ")[0]
+                        end
+		elsif h.include?("EM: C")
+			tmp = info[i]
+                        tmp.split(",").each do |t|
+                                alleles["C"]["Hisat"] << t.split(" ")[0]
+                        end
 		end
+
 	end
 
 end
@@ -156,7 +167,7 @@
 results = []
 results << [ "Allele", "xHLA (Nicht-kommerziell)", "Hisat", "Optitype" ]
 alleles.keys.each do |k|
-	results << [ k, alleles[k]["xHLA"].join(", "), "", alleles[k]["Optitype"].join(", ") ]
+	results << [ k, alleles[k]["xHLA"].sort.join(", "), alleles[k]["Hisat"].sort.join(", "), alleles[k]["Optitype"].sort.join(", ") ]
 end
 
 t = pdf.make_table( 

conf/test.config

@@ -1,5 +1,5 @@
 params {
 	samples = "https://raw.githubusercontent.com/ikmb/nf-testdata/master/hla/samples.csv"
-	tools = 'xhla,optitype'
+	tools = 'xhla,optitype,hisat'
 	run_name = "Testrun"
 }

docs/usage.md

@@ -23,7 +23,7 @@ patientID;sampleID;libraryID;rgID;R1;R2
 PatientA;Sample1;22Oct21_S3;C41232CXX.1.22Oct21_S3;/path/to/R1.fastq.gz;/path/to/R2.fastq.gz
 ```
 
-This is the preffered input option as it provide more control over the naming and grouping of the data. 
+This is the preferred input option as it provide more control over the naming and grouping of the data. 
 
 A simple ruby script is included with this pipeline to produce this file from a folder of FastQ files. However, please check 
 the output to make sure that it correctly recognized the file names etc.
@@ -65,7 +65,7 @@ nextflow run ikmb/hla --samples Samples.csv --tools 'hisat,xhla,optitype'
 Supported tools:
 
 * [xHLA](https://github.com/humanlongevity/HLA) (xhla)
-* [Hisat-genotype](https://daehwankimlab.github.io/hisat-genotype/) (hisat)
+* [Hisat-genotype](https://daehwankimlab.github.io/hisat-genotype/) (hisat)   SLOW!!
 * [Optitype](https://github.com/FRED-2/OptiType) (optitype)
 
 ### `--run_name`

main.nf

@@ -34,7 +34,7 @@ multiqc_report = Channel.from([])
 
 log.info "IKMB HLA Pipeline"
 log.info "${workflow.manifest.description}              v${params.version}"
-log.info "Nextflow Version:			                     $workflow.nextflow.version"
+log.info "Nextflow Version:			                     		$workflow.nextflow.version"
 log.info "Tools requested:						${params.tools}"
 log.info "------------------------------------------"
 

modules/hisat/report.nf

@@ -1,5 +1,9 @@
 process HISAT_REPORT {
 
+	tag "${meta.patient_id}|${meta.sample_id}"
+
+	publishDir "${params.outdir}/${meta.patient_id}/${meta.sample_id}", mode: 'copy'
+
 	input:
 	tuple val(meta),path(result)
 
@@ -11,7 +15,7 @@ process HISAT_REPORT {
 	report = "${meta.patient_id}_${meta.sample_id}.hisat.tsv"
 
 	"""
-		hisatgenotype_toolkit parse-results --csv --in-dir $result > $report
+		hisatgenotype_toolkit parse-results --csv --in-dir $result --output-file $report
 	"""
 
 }

modules/reporting.nf

@@ -1,5 +1,7 @@
 process REPORT {
 
+	tag "${meta.patient_id}|${meta.sample_id}"
+
 	publishDir "${params.outdir}/${meta.patient_id}/${meta.sample_id}", mode: 'copy'
 
 	input:

nextflow.config

@@ -53,7 +53,7 @@ dag {
         file = "${params.outdir}/pipeline_info/pipeline_dag.svg"
 }
 
-process.container = 'ikmb/hla:devel'
+process.container = 'ikmb/hla:1.0'
 
 profiles {
 	standard {

subworkflows/hisat.nf

@@ -1,6 +1,6 @@
 include { HISAT_GENOTYPE } from "./../modules/hisat/genotype"
 include { HISAT_REPORT } from "./../modules/hisat/report"
-
+include { FASTQ_MERGE } from "./../modules/fastq_merge"
 
 workflow HISAT_TYPING {