simplify tronflow integration + add test for single reads sequencing

Makefile

@@ -10,14 +10,22 @@ clean:
 test:
 	nextflow main.nf --help
 	nextflow main.nf -profile test,conda --name ERR4145453 \
-	--output `pwd`/output \
+	--output `pwd`/output/test1 \
 	--fastq1 `pwd`/test_data/ERR4145453_1.fastq.gz \
 	--fastq2 `pwd`/test_data/ERR4145453_2.fastq.gz
+	nextflow main.nf -profile test,conda --name ERR4145453 \
+	--output `pwd`/output/test2 \
+	--fastq1 `pwd`/test_data/ERR4145453_1.fastq.gz
 
 
 check:
-	test -s output/ERR4145453.bam || { echo "Missing BAM output file!"; exit 1; }
-	test -s output/ERR4145453.preprocessed.bam || { echo "Missing BAM output file!"; exit 1; }
-	test -s output/ERR4145453.vcf || { echo "Missing BAM output file!"; exit 1; }
-	test -s output/ERR4145453.normalized.vcf || { echo "Missing BAM output file!"; exit 1; }
-	test -s output/ERR4145453.annotated.vcf || { echo "Missing BAM output file!"; exit 1; }
+	test -s output/test1/ERR4145453.bam || { echo "Missing test 1 BAM output file!"; exit 1; }
+	test -s output/test1/ERR4145453.preprocessed.bam || { echo "Missing test 1 BAM output file!"; exit 1; }
+	test -s output/test1/ERR4145453.vcf || { echo "Missing test 1 VCF output file!"; exit 1; }
+	test -s output/test1/ERR4145453.normalized.vcf || { echo "Missing test 1 VCF output file!"; exit 1; }
+	test -s output/test1/ERR4145453.annotated.vcf || { echo "Missing test 1 VCF output file!"; exit 1; }
+	test -s output/test2/ERR4145453.bam || { echo "Missing test 2 BAM output file!"; exit 1; }
+	test -s output/test2/ERR4145453.preprocessed.bam || { echo "Missing test 2 BAM output file!"; exit 1; }
+	test -s output/test2/ERR4145453.vcf || { echo "Missing test 2 VCF output file!"; exit 1; }
+	test -s output/test2/ERR4145453.normalized.vcf || { echo "Missing test 2 VCF output file!"; exit 1; }
+	test -s output/test2/ERR4145453.annotated.vcf || { echo "Missing test 2 VCF output file!"; exit 1; }

main.nf

@@ -61,10 +61,12 @@ process alignment {
 	    file "${name}.bam"
 
     """
-    echo "${name}\t${fastq1}\t${fastq2}" > bwa_input_files.txt
-
+    # --input_files needs to be forced, otherwise it is inherited from profile in tests
     nextflow run tron-bioinformatics/tronflow-bwa -r ${params.tronflow_bwa_version} \
-    --input_files bwa_input_files.txt \
+    --input_name ${name} \
+    --input_fastq1 ${fastq1} \
+    --input_fastq2 ${fastq2} \
+    --input_files false \
     --algorithm mem \
     --library ${library} \
     --output . \
@@ -90,13 +92,14 @@ process bamPreprocessing {
 	    file "${name}.preprocessed.bai"
 
     """
-    echo "${name}\tnormal\t${bam}" > bam_preprocessing_input_files.txt
-
+    # --input_files, --known_indels1 and --known_indels2 needs to be forced, otherwise it is inherited from test profile
     nextflow run tron-bioinformatics/tronflow-bam-preprocessing -r ${params.tronflow_bam_preprocessing_version} \
-    --input_files bam_preprocessing_input_files.txt \
+    --input_bam ${bam} \
+    --input_files false \
     --output . \
     --reference ${params.reference} \
-    --skip_bqsr --skip_realignment --skip_metrics \
+    --skip_bqsr --skip_metrics \
+    --known_indels1 false --known_indels2 false \
     --prepare_bam_cpus ${params.cpus} --prepare_bam_memory ${params.memory} \
     --mark_duplicates_cpus ${params.cpus} --mark_duplicates_memory ${params.memory} \
     -profile ${workflow.profile} \
@@ -139,10 +142,10 @@ process variantNormalization {
 	    file "${name}.normalized.vcf"
 
     """
-    echo "${name}\t${vcf}" > vcf_normalization_input_files.txt
-
+    # --input_files needs to be forced, otherwise it is inherited from profile in tests
     nextflow run tron-bioinformatics/tronflow-variant-normalization -r ${params.tronflow_variant_normalization_version} \
-    --input_files vcf_normalization_input_files.txt \
+    --input_vcf ${vcf} \
+    --input_files false \
     --output . \
     --reference ${params.reference} \
     -profile ${workflow.profile} \

nextflow.config

@@ -4,9 +4,9 @@
  * -------------------------------------------------
  */
 
-params.tronflow_bwa_version = "v1.2.0"
-params.tronflow_bam_preprocessing_version = "v1.4.0"
-params.tronflow_variant_normalization_version = "v1.0.1"
+params.tronflow_bwa_version = "v1.3.0"
+params.tronflow_bam_preprocessing_version = "v1.5.0"
+params.tronflow_variant_normalization_version = "v1.1.0"
 
 params.reference = "$baseDir/test_data/Sars_cov_2.ASM985889v3.dna.toplevel.fa"
 params.gff = "$baseDir/test_data/Sars_cov_2.ASM985889v3.101.gff3"