add new fusion processes

STARFusion/1.9.1/STARFusion.nf

@@ -1,24 +1,25 @@
-process STAR_Fusion {
-    tag {"STAR_Fusion_${sample_id}"}
-	publishDir "${outdir}/STAR_Fusion", mode: 'copy'
-	shell = ['/bin/bash', '-euo', 'pipefail']
-	label 'process_medium'
+process starFusion {
+
+    tag { "STAR_Fusion - ${sample_id}" } 
+    publishDir "${outdir}/${sampleProject}/STAR_fusion", mode: 'copy'
+    label 'process_starfusion'
 
     input:
-        tuple val(sample_id), file(read1), file(read2)
-		path genome_lib
+    tuple val(sample_id), file(reads)
+	path genome_lib
 
     output:
     tuple val(sample_id), val(outdir)
-        file("${sample_id}_star-fusion.tsv"),
-        file("${sample_id}_star-fusion.abridged.tsv")
+    file("${sample_id}_star-fusion.tsv"),
+    file("${sample_id}_star-fusion.abridged.tsv")
 
     script:
     """
 	STAR-Fusion \
 	    --genome_lib_dir ${genome_lib} \
-        --left_fq ${read1} \
-        --right_fq ${read2} \
+        --left_fq ${reads[0]} \
+        --right_fq ${reads[1]} \
+        --CPU ${task.cpus} \
     	--FusionInspector inspect \
     	--examine_coding_effect \
         --denovo_reconstruct \

arriba/2.1.0/Arriba.nf

@@ -1,47 +1,60 @@
-process Arriba {
-    tag {"Arriba ${sample_id}"}
-	publishDir "${outdir}/Arriba", mode: 'copy'
-	shell = ['/bin/bash', '-euo', 'pipefail']
+process arriba {
+
+	tag { "Arriba - ${sample_id}" } 
+    publishDir "${outdir}/${sampleProject}/Arriba", mode: 'copy'
+    label 'process_arriba'
 
     input:
-        tuple val(sample_id), file(reads)
-        path star_idx
-    	path blacklist
-    	path assembly
-    	path annotation
-    	val outdir
-        val opt_args
+	tuple val(sample_id), file(reads)
+	path star_idx
+	path blacklist
+	path assembly
+	path annotation
+	path known
+	path pdomains
+	val outdir
+	val opt_args
 
     output:
     tuple val(sample_id),
-        file("${sample_id}.arriba.fusions.tsv"),
-        file("${sample_id}.arriba.fusions.discarded.tsv")
+	file("${sample_id}.arriba.fusions.tsv"),
+	file("${sample_id}.arriba.fusions.discarded.tsv")
 
     script:
     """
-	${opt_args}
-        --genomeLoad NoSharedMemory \
-    	--outStd BAM_SortedByCoordinate \
-    	--outSAMunmapped Within \
-    	--outBAMcompression 0 \
-    	--outFilterMultimapNmax 50 \
-    	--peOverlapNbasesMin 10 \
-    	--alignSplicedMateMapLminOverLmate 0.5 \
-    	--alignSJstitchMismatchNmax 5 -1 5 5 \
-	    --chimJunctionOverhangMin 10 \
-    	--chimScoreDropMax 30 \
-    	--chimScoreJunctionNonGTAG 0 \
-    	--chimScoreSeparation 1 \
-    	--chimSegmentReadGapMax 3 \
-	    --chimMultimapNmax 50 |
-
-
-    arriba -b ${blacklist}.tsv.gz \
-	    -x /dev/stdin \
+	STAR \
+		--runThreadN 8 \
+		--genomeDir ${star_idx} \
+		--genomeLoad NoSharedMemory \
+		--readFilesIn ${reads} \
+		--runThreadN ${task.cpus} \
+		--readFilesCommand zcat \
+		--outStd BAM_Unsorted \
+		--outSAMtype BAM Unsorted \
+		--outSAMunmapped Within \
+		--outBAMcompression 0 \
+		--outFilterMultimapNmax 50 \
+		--peOverlapNbasesMin 10 \
+		--alignSplicedMateMapLminOverLmate 0.5 \
+		--alignSJstitchMismatchNmax 5 -1 5 5 \
+		--chimSegmentMin 10 \
+		--chimOutType WithinBAM HardClip \
+		--chimJunctionOverhangMin 10 \
+		--chimScoreDropMax 30 \
+		--chimScoreJunctionNonGTAG 0 \
+		--chimScoreSeparation 1 \
+		--chimSegmentReadGapMax 3 \
+		--chimMultimapNmax 50 |
+	arriba \
+    	-x /dev/stdin \
 	    -o ${sample_id}.arriba.fusions.tsv \
 	    -O ${sample_id}.arriba.fusions.discarded.tsv \
-	    -a ${assembly}.fa \
-	    -g ${annotation}.gtf \		
+		-a ${annotation}.gtf \
+		-g ${annotation}.gtf \
+		-b ${blacklist}.tsv.gz \
+		-k ${known}.tsv.gz \
+		-t ${known}.tsv.gz \
+		-p ${pdomains}.gff3	
     """
 }