Merge pull request #284 from srl147/botseq

Botseq/Duplex-Seq/Nano-Seq

Changes

@@ -1,6 +1,9 @@
 CHANGES LOG
 -----------
 
+ - renamed markdup_botseq.json markdup_duplexseq.json
+ - add markdup_botseq.json
+
 0.28.2
  - move samtools calmd to correct position downstream of coord sort, and make calmd -Q flag (quiet) the default (alignment with markdup_method:none)
 

MANIFEST

@@ -33,6 +33,10 @@ data/vtlib/seqchksum_realign.json
 data/vtlib/split_by_chromosome.json
 data/vtlib/star_alignment.json
 data/vtlib/tophat2_alignment.json
+data/vtlib/markdup_biobambam.json
+data/vtlib/markdup_duplexseq.json
+data/vtlib/markdup_picard.json
+data/vtlib/markdup_samtools.json
 examples/bwa_aln_cfg.png
 examples/bwa_mem/bwa_mem_alignment.vtf
 examples/bwa_mem/generic_alignment_with_phix.vtf

data/vtlib/final_output_prep.json

@@ -265,6 +265,7 @@
 				"samtools":"markdup_samtools.json",
 				"picard":"markdup_picard.json",
 				"biobambam":"markdup_biobambam.json",
+				"duplexseq":"markdup_duplexseq.json",
 				"none":"markdup_none.json"
 			}
 		}

data/vtlib/markdup_duplexseq.json

@@ -0,0 +1,38 @@
+{
+"version":"2.0",
+"description":"steps in the alignment pipeline to post-process bam files produced by the AlignmentFilter",
+"subgraph_io":{
+	"ports":{
+		"inputs":{ "_stdin_":"bamsort_coord" },
+		"outputs":{ "_stdout_":"bammarkduplicates" }
+	}
+},
+"nodes":[
+	{
+		"id":"bamsort_coord_output",
+		"type":"RAFILE",
+		"name": "bamsort_coord.bam"
+	},
+	{
+		"id":"bamsort_coord",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"cmd": [ {"subst":"bsc_executable", "required":"yes", "ifnull":"bamsormadup"}, {"subst":"bsmd_threads"}, "SO=coordinate", "verbose=0", "fixmate=1", "rcsupport=1", {"subst":"bs_tmpfile_flag"} ]
+	},
+	{
+		"id":"bammarkduplicates",
+		"comment":"default tool bammarkduplicatesopt from Biobambam >= 2.0.65",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"cmd": [ "bammarkduplicatesopt", "level=0", "verbose=0", {"subst":"bmd_tmpfile_flag"}, {"subst":"bmd_metrics_file_flag"},
+                         {"subst":"optical_distance_flag","ifnull":{"subst_constructor":{"vals":[ "optminpixeldif", {"subst":"markdup_optical_distance_value","required":false,"ifnull":2500} ], "postproc":{"op":"concat","pad":"="}}}} ]
+	}
+],
+"edges":[
+
+	{ "id":"coordsort_todisk", "from":"bamsort_coord", "to":"bamsort_coord_output" },
+	{ "id":"disk_tomarkdup", "from":"bamsort_coord_output", "to":"bammarkduplicates" }
+]
+}