diff --git a/data/vtlib/fastq_s2_pi.json b/data/vtlib/fastq_s2_pi.json index d6649d0f..72de2b58 100644 --- a/data/vtlib/fastq_s2_pi.json +++ b/data/vtlib/fastq_s2_pi.json @@ -60,20 +60,14 @@ "select_range":[1], "default":"off", "cases":{ - "on":"EXEC", + "on":"VTFILE", "off":"INACTIVE" } }, "use_STDIN": true, "use_STDOUT": true, - "cmd": [ - {"subst":"bambi_executable", "required":true, "ifnull":"bambi"}, "read2tags", - "--tags", "rb,mb,br,rb,mb,br", - "--qtags", "rq,mq,bq,rq,mq,bq", - "--positions", "1:1:1:3,1:2:1:3,1:1:4:7,2:2:1:3,2:1:1:3,2:2:4:7", - "--compression-level", 0, - "--output-fmt", "bam" - ] + "name":"read2tags.json", + "node_prefix":"r2t_" } ], "edges":[ diff --git a/data/vtlib/read2tags.json b/data/vtlib/read2tags.json new file mode 100644 index 00000000..58424c49 --- /dev/null +++ b/data/vtlib/read2tags.json @@ -0,0 +1,54 @@ +{ +"version":"2.0", +"description":"read2tags for NanoSeq processing, including preparatory collation and reset", +"subgraph_io":{ + "ports":{ + "inputs":{"_stdin_":"collate"}, + "outputs":{ "_stdout_":"read2tags" } + } +}, +"nodes":[ + { + "id":"collate", + "type": "EXEC", + "use_STDIN": true, + "use_STDOUT": true, + "cmd": [ + {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "collate", + "--threads", {"subst":"s2_r2t_coll_threads","required":true,"ifnull":2}, + "-u", + "-O", + "-" + ] + }, + { + "id":"reset", + "type": "EXEC", + "use_STDIN": true, + "use_STDOUT": true, + "cmd": [ + {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "reset", + "--threads", {"subst":"s2_r2t_rs_threads","required":true,"ifnull":4}, + "--output-fmt", "BAM,level=0" + ] + }, + { + "id":"read2tags", + "type": "EXEC", + "use_STDIN": true, + "use_STDOUT": true, + "cmd": [ + {"subst":"bambi_executable", "required":true, "ifnull":"bambi"}, "read2tags", + "--tags", "rb,mb,br,rb,mb,br", + "--qtags", "rq,mq,bq,rq,mq,bq", + "--positions", "1:1:1:3,1:2:1:3,1:1:4:7,2:2:1:3,2:1:1:3,2:2:4:7", + "--compression-level", 0, + "--output-fmt", "bam" + ] + } +], +"edges":[ + { "id":"collate_to_reset", "from":"collate","to":"reset" }, + { "id":"reset_to_read2tags", "from":"reset", "to":"read2tags" } +] +}