Merge branch 'develop' into 'master'

Release v1.3.0

See merge request tron/tron-bam-preprocessing!12

Author: Pablo Riesgo Ferreiro

Makefile

@@ -9,10 +9,10 @@ clean:
 
 test:
 	nextflow main.nf -profile test,conda --output output/test1
-	#nextflow main.nf -profile test,conda --skip_bqsr --output output/test2
-	#nextflow main.nf -profile test,conda --skip_realignment --output output/test3
-	#nextflow main.nf -profile test,conda --skip_deduplication --output output/test4
-	#nextflow main.nf -profile test,conda --output output/test5 --skip_metrics
+	nextflow main.nf -profile test,conda --skip_bqsr --output output/test2
+	nextflow main.nf -profile test,conda --skip_realignment --output output/test3
+	nextflow main.nf -profile test,conda --skip_deduplication --output output/test4
+	nextflow main.nf -profile test,conda --output output/test5 --skip_metrics
 	nextflow main.nf -profile test,conda --output output/test6 --intervals false
 	nextflow main.nf -profile test,conda --output output/test7 --hs_metrics_target_coverage target_coverage.txt --hs_metrics_per_base_coverage per_base_coverage.txt
-	#nextflow main.nf -profile test,conda --output output/test8 --hs_metrics_target_coverage target_coverage.txt --hs_metrics_per_base_coverage per_base_coverage.txt --collect_hs_metrics_min_base_quality 10 --collect_hs_metrics_min_mapping_quality 10
+	nextflow main.nf -profile test,conda --output output/test8 --hs_metrics_target_coverage target_coverage.txt --hs_metrics_per_base_coverage per_base_coverage.txt --collect_hs_metrics_min_base_quality 10 --collect_hs_metrics_min_mapping_quality 10

environment.yml

@@ -1,11 +1,10 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: tronflow-bam-preprocessing-1.2.1
+name: tronflow-bam-preprocessing-1.3.0
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - openjdk=8.0.282
   - bioconda::gatk4=4.2.0.0
   - bioconda::gatk=3.8

main.nf

@@ -82,7 +82,7 @@ process prepareBam {
       set val(name),
         val("${bam.baseName}"),
         val(type), file("${bam.baseName}.prepared.bam"),
-        file("${bam.baseName}.prepared.bai")  into prepared_bams, prepared_bams_for_metrics, prepared_bams_for_hs_metrics
+        file("${bam.baseName}.prepared.bai")  into prepared_bams
 
     """
     mkdir tmp
@@ -128,7 +128,8 @@ if (!params.skip_deduplication) {
 
 	    output:
 	    	set val(name), val(bam_name), val(type),
-	    	    file("${bam.baseName}.dedup.bam"), file("${bam.baseName}.dedup.bam.bai") into deduplicated_bams
+	    	    file("${bam.baseName}.dedup.bam"), file("${bam.baseName}.dedup.bam.bai") into deduplicated_bams,
+	    	    deduplicated_bams_for_metrics, deduplicated_bams_for_hs_metrics
 	    	file("${bam.baseName}.dedup_metrics") optional true into deduplication_metrics
 
         script:
@@ -146,7 +147,7 @@ if (!params.skip_deduplication) {
 	}
 }
 else {
-    deduplicated_bams = prepared_bams
+    prepared_bams.into{ deduplicated_bams; deduplicated_bams_for_metrics; deduplicated_bams_for_hs_metrics}
 }
 
 if (! params.skip_metrics) {
@@ -160,7 +161,7 @@ if (! params.skip_metrics) {
             publishDir "${publish_dir}/${name}/metrics", mode: "copy"
 
             input:
-                set name, bam_name, type, file(bam), file(bai) from prepared_bams_for_hs_metrics
+                set name, bam_name, type, file(bam), file(bai) from deduplicated_bams_for_hs_metrics
 
             output:
                 file("*_metrics") optional true into txt_hs_metrics
@@ -200,7 +201,7 @@ if (! params.skip_metrics) {
 	    publishDir "${publish_dir}/${name}/metrics", mode: "copy"
 
 	    input:
-	    	set name, bam_name, type, file(bam), file(bai) from prepared_bams_for_metrics
+	    	set name, bam_name, type, file(bam), file(bai) from deduplicated_bams_for_metrics
 
 	    output:
 	        file("*_metrics") optional true into txt_metrics

nextflow.config

@@ -55,12 +55,12 @@ dag {
   //file = "${params.output}/pipeline_dag.svg"
 }
 
-VERSION = '1.2.1'
+VERSION = '1.3.0'
 DOI = 'https://zenodo.org/badge/latestdoi/358400957'
 
 manifest {
   name = 'TRON-Bioinformatics/tronflow-bam-preprocessing'
-  author = 'Pablo Riesgo Ferreiro'
+  author = 'Pablo Riesgo Ferreiro, Özlem Muslu'
   homePage = 'https://github.com/TRON-Bioinformatics/tronflow-bam-preprocessing'
   description = 'Picard and GATK BAM preprocessing pipeline'
   mainScript = 'main.nf'