Merge pull request #55 from dozy/cram_md5

add md5 outputs for both target and phix cram output

data/vtlib/alignment_wtsi_stage2_template.json

@@ -339,6 +339,22 @@
 			}
 		}
 	},
+	{
+		"id":"cram_md5",
+		"type":"OUTFILE",
+		"name":{"subst_param_name":"cram_md5",
+			"required":"yes",
+			"subst_constructor":{
+				"vals":[
+					{"subst_param_name":"outdatadir","required":"no","default":"."},
+					"/",
+					{"subst_param_name":"rpt","required":"yes"},
+					".cram.md5"
+				],
+				"postproc":{"op":"concat", "pad":""}
+			}
+		}
+	},
 	{
 		"id":"phix_cram",
 		"type":"OUTFILE",
@@ -355,6 +371,22 @@
 			}
 		}
 	},
+	{
+		"id":"phix_cram_md5",
+		"type":"OUTFILE",
+		"name":{"subst_param_name":"phix_cram_md5",
+			"required":"yes",
+			"subst_constructor":{
+				"vals":[
+					{"subst_param_name":"outdatadir","required":"no","default":"."},
+					"/",
+					{"subst_param_name":"rpt","required":"yes"},
+					"_phix.cram.md5"
+				],
+				"postproc":{"op":"concat", "pad":""}
+			}
+		}
+	},
 	{
 		"id":"out_bamcheck",
 		"type":"OUTFILE",
@@ -546,7 +578,7 @@
 		"to":"tee0"
 	},
 	{
-		"id":"t0_to_bamcollate2_ranking",
+		"id":"t0_to_bamcollate2_ranking_phix",
 		"from":"tee0:__PHIX_ALN_OUT__",
 		"to":"bamrecompress_input"
 	},
@@ -611,7 +643,7 @@
 		"to":"final_output_prep_target"
 	},
 	{
-		"id":"af_to_paf_target",
+		"id":"af_to_paf_phix",
 		"from":"alignment_filter:__PHIX_OUTBAM__",
 		"to":"final_output_prep_phix"
 	},
@@ -631,7 +663,7 @@
 		"to":"target_bam"
 	},
 	{
-		"id":"paf_to_bam",
+		"id":"paf_to_bam_phix",
 		"from":"final_output_prep_phix",
 		"to":"phix_bam"
 	},
@@ -640,12 +672,21 @@
 		"from":"final_output_prep_target:out_cram",
 		"to":"cram"
 	},
+	{
+		"id":"scramble_to_cram_md5",
+		"from":"final_output_prep_target:out_cram_md5",
+		"to":"cram_md5"
+	},
 	{
 		"id":"scramble_to_phix_cram",
 		"from":"final_output_prep_phix:out_cram",
 		"to":"phix_cram"
 	},
-
+	{
+		"id":"scramble_to_phix_cram_md5",
+		"from":"final_output_prep_phix:out_cram_md5",
+		"to":"phix_cram_md5"
+	},
 	{
 		"id":"bamcheck_out_target",
 		"from":"final_output_prep_target:out_bamcheck",

data/vtlib/final_output_prep.json

@@ -8,7 +8,8 @@
 		},
 		"outputs":{
 			"_stdout_":"bamrecompress",
-			"out_cram":"scramble",
+			"out_cram":"scramble_tee:__CRAM_OUT__",
+			"out_cram_md5":"scramble_md5",
 			"out_bamcheck":"bamcheck",
 			"out_stats_F0x900":"samtools_stats_F0x900",
 			"out_stats_F0xB00":"samtools_stats_F0xB00",
@@ -115,7 +116,21 @@
 		"use_STDOUT": true,
 		"cmd":"scramble -I bam -O cram -r __REFERENCE_GENOME_FASTA__"
 	},
-
+	{
+		"id":"scramble_tee",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": false,
+		"cmd":"teepot -w 30000 __CRAM_OUT__ __MD5_OUT__",
+		"comment":"allow a generous 500 minutes for the teepot timeout"
+	},
+	{
+		"id":"scramble_md5",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"cmd":"md5sum"
+	},
 	{
 		"id":"bamcheck",
 		"type":"EXEC",
@@ -317,10 +332,20 @@
 		"to":"bmd_multiway"
 	},
 	{
-		"id":"bmd_to_scramble",
+		"id":"bmdmw_to_scramble",
 		"from":"bmd_multiway:__SCRAMBLE_OUT__",
 		"to":"scramble"
 	},
+	{
+		"id":"scramble_to_scramble_tee",
+		"from":"scramble",
+		"to":"scramble_tee"
+	},
+	{
+		"id":"scramble_tee_to_md5",
+		"from":"scramble_tee:__MD5_OUT__",
+		"to":"scramble_md5"
+	},
 	{
 		"id":"bmd_to_bamcheck",
 		"from":"bmd_multiway:__BAMCHECK_OUT__",

data/vtlib/realignment_wtsi_template.json

@@ -293,7 +293,7 @@
 		"to":"tee0"
 	},
 	{
-		"id":"t0_to_bamcollate2_ranking",
+		"id":"t0_to_bamrecompress_input",
 		"from":"tee0:__PHIX_ALN_OUT__",
 		"to":"bamrecompress_input"
 	},
@@ -313,7 +313,7 @@
 		"to":"post_alignment_target:no_align_bam"
 	},
 	{
-		"id":"t0_to_bamcollate2_ranking",
+		"id":"t0_to_pre_alignment_target",
 		"from":"tee0:__TGT_ALN_OUT__",
 		"to":"pre_alignment_target"
 	},