Merge pull request #59 from wtsi-npg/devel

post-process md5 sum output

data/vtlib/final_output_prep.json

@@ -9,7 +9,7 @@
 		"outputs":{
 			"_stdout_":"bamrecompress",
 			"out_cram":"scramble_tee:__CRAM_OUT__",
-			"out_cram_md5":"scramble_md5",
+			"out_cram_md5":"postprocess_md5",
 			"out_bamcheck":"bamcheck",
 			"out_stats_F0x900":"samtools_stats_F0x900",
 			"out_stats_F0xB00":"samtools_stats_F0xB00",
@@ -131,6 +131,14 @@
 		"use_STDOUT": true,
 		"cmd":"md5sum"
 	},
+	{
+		"id":"postprocess_md5",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"cmd":["tr", "-d", " \\-\n"],
+		"comment":"the double-backslash is required to get the correct character set to the tr command"
+	},
 	{
 		"id":"bamcheck",
 		"type":"EXEC",
@@ -346,6 +354,11 @@
 		"from":"scramble_tee:__MD5_OUT__",
 		"to":"scramble_md5"
 	},
+	{
+		"id":"md5_to_postprocess",
+		"from":"scramble_md5",
+		"to":"postprocess_md5"
+	},
 	{
 		"id":"bmd_to_bamcheck",
 		"from":"bmd_multiway:__BAMCHECK_OUT__",