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always run samtools collate+reset before bambi read2tags
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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" } | ||
| ] | ||
| } |