diff --git a/bin/vtfp.pl b/bin/vtfp.pl
index d7c7ea44d..16aeb7c49 100755
--- a/bin/vtfp.pl
+++ b/bin/vtfp.pl
@@ -678,18 +678,13 @@ sub fetch_param_entry {
 		}
 	}
 
-	my $candidate;
 	if(exists $param_entry->{_value}) {
-		$candidate = $param_entry;   # already evaluated, return cached value (allowing undef)
+		return $param_entry;   # already evaluated, return cached value (allowing undef)
 	}
 
 	push @{$aux->{irp}}, $param_name;
 	$retval = resolve_subst_constructor($param_name, $param_entry->{subst_constructor}, $params, $ewi, $aux);
 
-	if(not $retval and $candidate) {
-		$retval = $candidate->{_value};
-	}
-
 	if(defined $retval) {
 		$param_entry->{_value} = $retval;
 	}
diff --git a/data/vtlib/bambi_i2b.json b/data/vtlib/bambi_i2b.json
new file mode 100644
index 000000000..80d52de3d
--- /dev/null
+++ b/data/vtlib/bambi_i2b.json
@@ -0,0 +1,119 @@
+{
+"version":"2.0",
+"description":"This pipeline starts with Illumina2Bam, and ends by running SplitBamByReadGroup to create separate BAM files for each sample.",
+"subgraph_io":{
+	"ports":{
+		"inputs":{},
+		"outputs":{
+			"_stdout_":"i2b"
+		}
+	}
+},
+"subst_params":[
+	{"id":"rpt","description":"Run/Position/TagIndex, though here it is generally only Run/Position. Used in defaults/constructors for i2b_rg,decoder_metrics,md5_file,seqchksum_file,spatial_filter_file and filtered_bam"},
+	{"id":"i2b_run_path","description":"path to runfolder. Provides a base on which i2b_runfolder_path can be constructed"},
+	{"id":"i2b_runfolder","description":"runfolder directory. Provides a base on which platform unit and i2b_runfolder_path can be constructed"},
+	{"id":"i2b_runfolder_path","description":"full path to runfolder. Provides a base on which platform unit, intensities directory and (indirectly) basecalls directories can be constructed", 
+		"subst_constructor":{
+			"vals":[ {"subst":"i2b_run_path","required":"yes"}, {"subst":"i2b_runfolder","required":"yes"} ],
+			"postproc":{"op":"concat","pad":"/"}
+		}
+
+	},
+	{
+		"id":"i2b_intensity_dir",
+		"required":"yes",
+		"description":"Illumina intensities directory including config xml file, and clocs, locs or pos files under lane directory, using Data/Intensities directory under runfolder if not given",
+		"subst_constructor":{
+			"vals":[ {"subst":"i2b_runfolder_path","required":"yes"}, "/", {"subst":"i2b_data_intensities_dir_suffix","ifnull":"Data/Intensities"} ],
+			"postproc":{"op":"concat","pad":""}
+		}
+	},
+	{
+		"id":"i2b_basecalls_dir",
+		"required":"no",
+		"description":"Illumina basecalls directory including config xml file, and filter files, bcl, maybe scl files under lane cycle directory, using BaseCalls directory under intensities if not given.",
+		"subst_constructor":{
+			"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_basecalls_dir_suffix","ifnull":"BaseCalls"} ],
+			"postproc":{"op":"concat","pad":""}
+		}
+	},
+	{
+		"id":"i2b_bam_basecalls_dir",
+		"required":"no",
+		"description":"full path to the BAM_basecalls directory; a default parameter value for the tag_metrics qc check",
+		"subst_constructor":{
+			"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_bam_basecalls_dir_suffix","required":"yes"} ],
+			"postproc":{"op":"concat","pad":""}
+		}
+	},
+	{"id":"i2b_lane","required":"yes","comment":"Lane number"},
+	{
+		"id":"i2b_pu",
+		"description":"The platform unit, using runfolder name plus lane number if not given",
+		"subst_constructor":{
+			"vals":[ {"subst":"i2b_runfolder"}, "_", {"subst":"i2b_lane"} ],
+			"postproc":{"op":"concat","pad":""}
+		}
+	},
+	{"id":"i2b_library_name","description":"The name of the sequenced library"},
+	{"id":"i2b_rg", "description":"ID used to link RG header record with RG tag in SAM record", "default":{"subst":"rpt"}},
+	{"id":"i2b_bc_seq_val","required":"no","description":"Tag name for barcode sequence. Illumina2bam default is BC"},
+	{"id":"i2b_bc_qual_val","required":"no","description":"Tag name for barcode quality. Illumina2bam default is QT"},
+	{"id":"i2b_sec_bc_seq_val","required":"no","description":"Tag name for second  barcode sequence. Illumina2bam default is null"},
+	{"id":"i2b_sec_bc_qual_val","required":"no","description":"Tag name for second barcode quality. Illumina2bam default is null"},
+	{"id":"i2b_study_name","description":"The name of the study"},
+	{
+		"id":"i2b_sample_aliases",
+		"default":"UNSPECIFIED",
+		"comment":"produces a comma-separated string from array of i2b_sample_alias values",
+		"subst_constructor":{
+			"vals":{"subst":"i2b_sample_alias", "ifnull":["UNSPEC"]},
+			"postproc":{"op":"concat","pad":","}
+		}
+	}
+],
+"nodes":[
+	{
+		"id":"i2b",
+		"type":"EXEC",
+		"description":"Create the initial BAM file from the data generated by the Illumina machine using bambi i2b",
+		"use_STDIN":false,
+		"use_STDOUT":true,
+		"cmd":[
+			"bambi",
+			"i2b",
+			{"subst":"i2b_intensity_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--intensity-dir", {"subst":"i2b_intensity_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_basecalls_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--basecalls-dir", {"subst":"i2b_basecalls_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_lane_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--lane", {"subst":"i2b_lane","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_pu_flag","ifnull":{"subst_constructor":{"vals":[ "--platform-unit", {"subst":"i2b_pu"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_rg_flag","ifnull":{"subst_constructor":{"vals":[ "--read-group-id", {"subst":"i2b_rg"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--barcode-tag", {"subst":"i2b_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--quality-tag", {"subst":"i2b_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_sec_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-barcode-tag", {"subst":"i2b_sec_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_sec_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-quality-tag", {"subst":"i2b_sec_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_first_tile_flag","ifnull":{"subst_constructor":{"vals":[ "--first-tile", {"subst":"i2b_first_tile"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_tile_limit_flag","ifnull":{"subst_constructor":{"vals":[ "--tile-limit", {"subst":"i2b_tile_limit"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_library_flag","ifnull":{"subst_constructor":{"vals":[ "--library-name", {"subst":"i2b_library_name"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_study_name_flag","ifnull":{"subst_constructor":{"vals":[ "--study-name", {"subst":"i2b_study_name"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_sample_alias_flag","ifnull":{"subst_constructor":{"vals":[ "--sample-alias", {"subst":"i2b_sample_aliases"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_bc_read_flag","ifnull":{"subst_constructor":{"vals":[ "--bc-read", {"subst":"i2b_bc_read"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_first_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_final_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_first_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_final_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_first_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_0"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_final_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_0"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_first_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_1"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_final_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_1"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_thread_count_flag","ifnull":{"subst_constructor":{"vals":[ "--threads", {"subst":"i2b_thread_count"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"subst":"i2b_tqlen_flag","ifnull":{"subst_constructor":{"vals":[ "--queue-len", {"subst":"i2b_tqlen"} ],"postproc":{"op":"concat","pad":"="}}}},
+			{"select":"i2b_nocall_qual_switch", "required":true, "select_range":[1], "default":"off", "cases":{ "on": "--nocall-quality", "off":[]}},
+			{"subst":"i2b_arbitrary_flags", "comment":"this allows arbitrary sets of flag strings to be inserted in the command" },
+			"--output-file=-",
+			"--compression-level=0"
+		]
+	}
+],
+"edges":[]
+}
diff --git a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json
index 52aa889cc..dd6c56255 100644
--- a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json
+++ b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json
@@ -2,117 +2,25 @@
 "description":"This pipeline starts with Illumina2Bam, and ends by running SplitBamByReadGroup to create separate BAM files for each sample.",
 "version":"2.0",
 "subst_params":[
-	{"id":"rpt","description":"Run/Position/TagIndex, though here it is generally only Run/Position. Used in defaults/constructors for i2b_rg,decoder_metrics,md5_file,seqchksum_file,spatial_filter_file and filtered_bam"},
-	{"id":"i2b_run_path","description":"path to runfolder. Provides a base on which i2b_runfolder_path can be constructed"},
-	{"id":"i2b_runfolder","description":"runfolder directory. Provides a base on which platform unit and i2b_runfolder_path can be constructed"},
-	{"id":"i2b_runfolder_path","description":"full path to runfolder. Provides a base on which platform unit, intensities directory and (indirectly) basecalls directories can be constructed", 
-		"subst_constructor":{
-			"vals":[ {"subst":"i2b_run_path","required":"yes"}, {"subst":"i2b_runfolder","required":"yes"} ],
-			"postproc":{"op":"concat","pad":"/"}
-		}
-
-	},
-	{
-		"id":"i2b_intensity_dir",
-		"required":"yes",
-		"description":"Illumina intensities directory including config xml file, and clocs, locs or pos files under lane directory, using Data/Intensities directory under runfolder if not given",
-		"subst_constructor":{
-			"vals":[ {"subst":"i2b_runfolder_path","required":"yes"}, "/", {"subst":"i2b_data_intensities_dir_suffix","ifnull":"Data/Intensities"} ],
-			"postproc":{"op":"concat","pad":""}
-		}
-	},
-	{
-		"id":"i2b_basecalls_dir",
-		"required":"no",
-		"description":"Illumina basecalls directory including config xml file, and filter files, bcl, maybe scl files under lane cycle directory, using BaseCalls directory under intensities if not given.",
-		"subst_constructor":{
-			"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_basecalls_dir_suffix","ifnull":"BaseCalls"} ],
-			"postproc":{"op":"concat","pad":""}
-		}
-	},
-	{
-		"id":"i2b_bam_basecalls_dir",
-		"required":"no",
-		"description":"full path to the BAM_basecalls directory; a default parameter value for the tag_metrics qc check",
-		"subst_constructor":{
-			"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_bam_basecalls_dir_suffix","required":"yes"} ],
-			"postproc":{"op":"concat","pad":""}
-		}
-	},
-	{"id":"i2b_lane","required":"yes","comment":"Lane number"},
-	{
-		"id":"i2b_pu",
-		"description":"The platform unit, using runfolder name plus lane number if not given",
-		"subst_constructor":{
-			"vals":[ {"subst":"i2b_runfolder"}, "_", {"subst":"i2b_lane"} ],
-			"postproc":{"op":"concat","pad":""}
-		}
-	},
-	{"id":"i2b_library_name","description":"The name of the sequenced library"},
-	{"id":"i2b_rg", "description":"ID used to link RG header record with RG tag in SAM record", "default":{"subst":"rpt"}},
-	{"id":"i2b_bc_seq_val","required":"no","description":"Tag name for barcode sequence. Illumina2bam default is BC"},
-	{"id":"i2b_bc_qual_val","required":"no","description":"Tag name for barcode quality. Illumina2bam default is QT"},
-	{"id":"i2b_sec_bc_seq_val","required":"no","description":"Tag name for second  barcode sequence. Illumina2bam default is null"},
-	{"id":"i2b_sec_bc_qual_val","required":"no","description":"Tag name for second barcode quality. Illumina2bam default is null"},
-	{"id":"i2b_study_name","description":"The name of the study"},
-	{
-		"id":"i2b_sample_aliases",
-		"default":"UNSPECIFIED",
-		"comment":"produces a comma-separated string from array of i2b_sample_alias values",
-		"subst_constructor":{
-			"vals":{"subst":"i2b_sample_alias", "ifnull":["UNSPEC"]},
-			"postproc":{"op":"concat","pad":","}
-		}
-	},
+	{"id":"s1_runfolder_path","required":"yes","default":{"subst":"i2b_runfolder_path"}, "comment":"Stage1 runfolder path"},
+	{"id":"s1_basecalls_dir","required":"yes","default":{"subst":"i2b_basecalls_dir"}, "comment":"Stage1 BAM_basecalls directory"},
+	{"id":"s1_lane","required":"yes","default":{"subst":"i2b_lane"}, "comment":"Stage1 lane number"},
 	{"id":"qc_check_id_run","required":"yes"},
-	{"id":"qc_check_position","required":"yes","default":{"subst":"i2b_lane"}},
-	{"id":"qc_check_qc_in_dir","required":"yes","default":{"subst_constructor":{"vals":[{"subst":"i2b_runfolder_path"}, "Data/Intensities", {"subst":"i2b_bam_basecalls_dir"}],"postproc":{"op":"concat","pad":"/"}}}},
+	{"id":"qc_check_position","required":"yes","default":{"subst":"s1_lane"}},
+	{"id":"qc_check_qc_in_dir","required":"yes","default":{"subst_constructor":{"vals":[{"subst":"s1_runfolder_path"}, "Data/Intensities", {"subst":"s1_bam_basecalls_dir"}],"postproc":{"op":"concat","pad":"/"}}}},
 	{"id":"qc_check_qc_out_dir","required":"yes","default":{"subst_constructor":{"vals":[{"subst":"qc_check_qc_in_dir"}, "no_cal/archive/qc"],"postproc":{"op":"concat","pad":"/"}}}},
-	{"id":"run_lane_label", "description":"label constructed from id_run and position", "default":{"subst_constructor":{"vals":[{"subst":"qc_check_id_run"}, "_", {"subst":"i2b_lane"}],"postproc":{"op":"concat","pad":""}}}},
+	{"id":"run_lane_label", "description":"label constructed from id_run and position", "default":{"subst_constructor":{"vals":[{"subst":"qc_check_id_run"}, "_", {"subst":"s1_lane"}],"postproc":{"op":"concat","pad":""}}}},
 	{"id":"s1_output_format", "description":"output format for deplexed reads (bam/cram/etc)", "default":"cram"}
 ],
 "nodes":[
-	{
-		"id":"illumina2bam",
-		"type":"EXEC",
-		"use_STDIN":false,
-		"use_STDOUT":true,
-		"comment":"Actual executable used depends on the value of the 12b_implementation parameter: java - use illumina2bam (default); bambi - use new bambi i2b",
-		"cmd":[
-				"bambi",
-				"i2b",
-				{"subst":"i2b_intensity_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--intensity-dir", {"subst":"i2b_intensity_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_basecalls_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--basecalls-dir", {"subst":"i2b_basecalls_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_lane_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--lane", {"subst":"i2b_lane","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_pu_flag","ifnull":{"subst_constructor":{"vals":[ "--platform-unit", {"subst":"i2b_pu"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_rg_flag","ifnull":{"subst_constructor":{"vals":[ "--read-group-id", {"subst":"i2b_rg"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--barcode-tag", {"subst":"i2b_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--quality-tag", {"subst":"i2b_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_sec_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-barcode-tag", {"subst":"i2b_sec_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_sec_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-quality-tag", {"subst":"i2b_sec_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_first_tile_flag","ifnull":{"subst_constructor":{"vals":[ "--first-tile", {"subst":"i2b_first_tile"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_tile_limit_flag","ifnull":{"subst_constructor":{"vals":[ "--tile-limit", {"subst":"i2b_tile_limit"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_library_flag","ifnull":{"subst_constructor":{"vals":[ "--library-name", {"subst":"i2b_library_name"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_study_name_flag","ifnull":{"subst_constructor":{"vals":[ "--study-name", {"subst":"i2b_study_name"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_sample_alias_flag","ifnull":{"subst_constructor":{"vals":[ "--sample-alias", {"subst":"i2b_sample_aliases"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_bc_read_flag","ifnull":{"subst_constructor":{"vals":[ "--bc-read", {"subst":"i2b_bc_read"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_first_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_final_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_first_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_final_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_first_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_0"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_final_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_0"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_first_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_1"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_final_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_1"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_thread_count_flag","ifnull":{"subst_constructor":{"vals":[ "--threads", {"subst":"i2b_thread_count"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"subst":"i2b_tqlen_flag","ifnull":{"subst_constructor":{"vals":[ "--queue-len", {"subst":"i2b_tqlen"} ],"postproc":{"op":"concat","pad":"="}}}},
-				{"select":"i2b_nocall_qual_switch", "required":true, "select_range":[1], "default":"off", "cases":{ "on": "--nocall-quality", "off":[]}},
-				{"subst":"i2b_arbitrary_flags", "comment":"this allows arbitrary sets of flag strings to be inserted in the command" },
-				"--output-file=-",
-				"--compression-level=0"
-		],
-		"description":"Create the initial BAM file from the data generated by the Illumina machine"
-	},
+        {
+                "id":"produce_init_bam",
+                "type":"VTFILE",
+                "comment":"inputs: _stdin_ (bam), reference; outputs: _stdout_ (bam)",
+                "node_prefix":"pib_",
+                "name":{"subst":"s1_produce_init_bam_method", "required":true, "ifnull":{"select":"i2b_switch", "default":"i2b", "select_range":[1], "cases":{"i2b":"bambi_i2b.json", "reanalysis":"pib_reanalysis.json"}}},
+                "description":"subgraph containing i2b or reanalysis initialisation"
+        },
 	{
 		"id":"tee_i2b",
 		"type":"EXEC",
@@ -435,7 +343,7 @@
         }
 ],
 "edges":[
-	{ "id":"illumina2bam_to_ti2b", "from":"illumina2bam", "to":"tee_i2b" },
+	{ "id":"illumina2bam_to_ti2b", "from":"produce_init_bam", "to":"tee_i2b" },
 	{ "id":"ti2b_to_bamadapterfind", "from":"tee_i2b:baf", "to":"bamindexdecoder" },
 	{ "id":"decoder_to_metrics", "from":"bamindexdecoder:metrics_file", "to":"decoder_metrics" },
 	{ "id":"decoder_metrics_to_qc_tag_metrics", "from":"decoder_metrics", "to":"qc_tag_metrics_check" },
diff --git a/data/vtlib/pib_reanalysis.json b/data/vtlib/pib_reanalysis.json
new file mode 100644
index 000000000..26e3723fb
--- /dev/null
+++ b/data/vtlib/pib_reanalysis.json
@@ -0,0 +1,123 @@
+{
+"version":"2.0",
+"description":"run bwa mem to to align input bam to supplied reference genome",
+"subgraph_io":{
+	"ports":{
+		"inputs":{},
+		"outputs":{
+			"_stdout_":"name_collate"
+		}
+	}
+},
+"subst_params":[],
+"nodes":[
+	{
+		"id":"merge",
+		"type":"EXEC",
+		"use_STDIN": false,
+		"use_STDOUT": true,
+		"cmd": [
+			"samtools",
+			"merge",
+			{"select":"pib_merge_input_order", "default":"coord", "select_range":[1], "cases":{
+				"coord":[],
+				"qname_alpha_numeric":"-n",
+				"qname_lexicographical":"-N"
+			}},
+			{"subst_constructor":{"vals":["-t", {"subst":"pib_sort_tag", "required":false}]}},
+			"-c",
+			"-r",
+			"-O", "BAM",
+			"-l", "0",
+			{"select":"s1_input_format", "default":"cram", "select_range":[1], "cases":{
+				"cram":["--input-fmt-option", "no_ref=1"],
+				"bam":[]
+			}},
+			{"subst":"merge_hdr_file_flag","ifnull":{
+								"subst_constructor":{
+									"vals":[
+										"-h",
+										{"subst":"merge_hdr_file","required":true, "ifnull":{"subst_constructor":{"vals":[{"subst":"reanalysis_root"}, "/auxdata/", {"subst":"qc_check_id_run"}, "/", {"subst":"qc_check_id_run"},"_", {"subst":"s1_lane"}, ".rg_hdr.sam"], "postproc":{"op":"concat","pad":""}}}}
+									]
+								}}},
+			{"subst":"pib_merge_arbitrary_flags", "required":false},
+			"-",
+			{"subst":"incrams"}
+		],
+		"description":"merge individual cram files from a sample into one bam file"
+	},
+	{
+		"id":"reheader",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"comment": "remove unwanted RG header lines",
+		"cmd": [
+			{"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "reheader",
+			"--no-PG",
+			"-c",
+			{"subst":"reheader_script","required":true,
+				"ifnull":{"subst_constructor":{"vals":[
+									"perl -ne \"(!/^\\@RG/ || /\\tID:",
+									{"subst":"reheader_rg_id", "required":true, "ifnull":{"subst":"i2b_rg"}},
+									"\\t/) && print;\""
+								], "postproc":{"op":"concat","pad":""}}}},
+			{"subst":"pib_reanalysis_reheader_extra_flags", "required":false},
+			"-"
+		]
+	},
+	{
+		"id":"reset",
+		"type":"EXEC",
+		"comment": "reset bam stream",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"cmd": [
+			{"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "reset",
+			{"subst":"reset_keep_tag_flag","ifnull":{
+								"subst_constructor":{
+									"vals":[
+										"--keep-tag",
+										{"subst":"reset_keep_tags","required":false, "ifnull":{"subst_constructor":{"vals":["RG","BC", "QT", "FI", "RT", "TC"], "postproc":{"op":"concat","pad":","}}}}
+									]
+								}}},
+			{"subst":"reset_reject_PG_flag","ifnull":{
+								"subst_constructor":{
+									"vals":[
+										"--reject-PG",
+										{"subst":"reset_reject_PG_id","required":false, "ifnull":"SCS"}
+									]
+								}}},
+			{"subst":"reset_output_format_flag","ifnull":{"subst_constructor":{"vals":["--output-fmt", {"subst":"reset_output_format", "ifnull":"BAM", "required":false}]}}},
+			"--threads", {"subst":"reset_threads","required":true,"ifnull":4},
+			{"subst":"reset_extra_flags", "required":false},
+			"-"
+		]
+	},
+	{
+		"id":"name_collate",
+		"type":"EXEC",
+		"use_STDIN": true,
+		"use_STDOUT": true,
+		"cmd": [
+			{"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "collate", "-O",
+			"-l", {"subst":"pib_reanalysis_collate_compression","required":true,"ifnull":["0"]},
+			"--threads", {"subst":"pib_reanalysis_collate_threads","required":true,"ifnull":4},
+			{"subst":"pib_reanalysis_collate_extra_flags", "required":false},
+			{"subst":"pib_collate_tempfile_flag","ifnull":{
+								"subst_constructor":{
+									"vals":[
+										"-T",
+										{"subst":"pib_collate_tempfile_prefix","required":false, "ifnull":{"subst_constructor":{"vals":[ {"subst":"qc_check_id_run"}, {"subst":"s1_lane"}, "collate_tmp"], "postproc":{"op":"concat","pad":"_"}}}}
+									]
+								}}},
+			"-"
+		]
+	}
+],
+"edges":[
+	{ "id":"merge_to_reheader", "from":"merge", "to":"reheader" },
+	{ "id":"reheader_to_reset", "from":"reheader", "to":"reset" },
+	{ "id":"reset_to_collate", "from":"reset", "to":"name_collate" }
+]
+}
diff --git a/t/10-vtfp-vtfile_v2.t b/t/10-vtfp-vtfile_v2.t
index d4cdedd47..f276a7af4 100644
--- a/t/10-vtfp-vtfile_v2.t
+++ b/t/10-vtfp-vtfile_v2.t
@@ -1,7 +1,7 @@
 use strict;
 use warnings;
 use Carp;
-use Test::More tests => 6;
+use Test::More tests => 7;
 use Test::Cmd;
 use File::Slurp;
 use Perl6::Slurp;
@@ -568,7 +568,7 @@ subtest 'multilevel_vtf_required_param' => sub {
 			{
 				id => 'vfile',
 				type => 'OUTFILE',
-				name => { subst_constructor => { vals => [ 'tmp.', {subst => 'ext', 'required' => 'true'} ], postproc => { op => 'concat', pad => ''} }, }
+				name => { subst_constructor => { vals => [ 'tmp.', {subst => 'ext', required => JSON::true} ], postproc => { op => 'concat', pad => ''} }, }
 			},
 		]
 	};
@@ -628,4 +628,186 @@ subtest 'multilevel_vtf_required_param' => sub {
 	is_deeply ($vtfp_results, $expected_result, 'multilevel local param reeval');
 };
 
+subtest 'multilevel_vtf_forced_undef' => sub {
+	plan tests => 4;
+
+	my $top_container = {
+				version => '2.0',
+				description => 'outermost of a nest of test VTFILEs',
+				subst_params => [
+					{ id => 'top_sp_contents', required => 'false', default => 'top SP' },
+					{
+						id => 'top_box',
+						required => 'false',
+						default => 'TB_DFLT',
+						subst_constructor => {
+							vals => [ 'TB [', {subst => 'top_sp_contents'}, '] TB' ],
+							postproc => {op => 'concat', pad => ''}
+						}
+					}
+				],
+				nodes => [
+					{
+						id => 'middle',
+						type => 'VTFILE',
+						node_prefix => 'mid_',
+						name => 'middle.json'
+					}
+				],
+				edges => []
+			};
+
+	my $middle = {
+			version => '2.0',
+			description => 'middle of a nest of test VTFILEs',
+			subst_params => [
+				{id => 'mid_sp_contents', required => 'false', default => 'mid SP'},
+				{
+					id => 'mid_box',
+					required => 'false',
+					default => 'MID_DFLT',
+					subst_constructor => {
+						vals => [ 'MIDB [', {subst => 'mid_sp_contents'}, '] MIDB' ],
+						postproc => {op => 'concat', pad => ''}
+					}
+				}
+			],
+			nodes => [
+					{
+						id => 'bottom',
+						type => 'VTFILE',
+						node_prefix => 'bot_',
+						name => 'bottom.json'
+					},
+					{
+						id => 'blather',
+						type => 'EXEC',
+						use_STDIN =>  'false',
+						use_STDOUT =>  'true',
+						cmd => [
+							'echo',
+							{subst => 'top_box'}, {subst => 'mid_box'}, {subst => 'bot_box'}
+						]
+					}
+			],
+			edges => []
+		};
+
+	my $bottom = {
+			version => '2.0',
+			description => 'innermost of a nest of test VTFILEs',
+			subst_params => [
+				{id => 'bot_sp_contents', required => 'false', default => 'bot SP'},
+				{
+					id => 'bot_box',
+					required => 'false',
+					default => 'BOT_DFLT',
+					subst_constructor => {
+						vals => [ 'BOTB [', {subst => 'bot_sp_contents'}, '] BOTB' ],
+						postproc => {op => 'concat', pad => ''}
+					}
+				}
+			],
+			nodes => [
+				{
+					id => 'haver',
+					type => 'EXEC',
+					use_STDIN => 'false',
+					use_STDOUT => 'true',
+					cmd => [
+						'echo',
+						{subst => 'top_box'}, {subst => 'mid_box'}, {subst => 'bot_box'}
+					]
+				}
+			],
+			edges => []
+		};
+
+	my ($template, $fn);
+	$fn = $template = $tdir.q[/10-vtfp-multilevel_vtf_forced_undef.json];
+	my $contents = to_json($top_container);
+	write_file($fn, $contents);
+
+	$fn = $tdir.q[/middle.json];
+	$contents = to_json($middle);
+	write_file($fn, $contents);
+
+	$fn = $tdir.q[/bottom.json];
+	$contents = to_json($bottom);
+	write_file($fn, $contents);
+
+	my $exit_status = $test->run(chdir => $test->curdir, args => qq[-no-absolute_program_paths -verbosity_level 0 -template_path $tdir $template]);
+	ok($exit_status>>8 == 0, "non-zero exit: $exit_status");
+	my $vtfp_results = from_json($test->stdout);
+	my $vtfp_err = $test->stderr;
+
+	my $expected_result = {
+          'version' => '2.0',
+          'edges' => [],
+          'nodes' => [
+                       {
+                         'id' => 'mid_blather',
+                         'type' => 'EXEC',
+                         'use_STDIN' => 'false',
+                         'use_STDOUT' => 'true',
+                         'cmd' => [
+                                    'echo',
+                                    'TB [top SP] TB',
+                                    'MIDB [mid SP] MIDB'
+                                  ]
+                       },
+                       {
+                         'id' => 'mid_bot_haver',
+                         'type' => 'EXEC',
+                         'use_STDIN' => 'false',
+                         'use_STDOUT' => 'true',
+                         'cmd' => [
+                                    'echo',
+                                    'TB [top SP] TB',
+                                    'MIDB [mid SP] MIDB',
+                                    'BOTB [bot SP] BOTB'
+                                  ],
+                       }
+                     ]
+        };
+	is_deeply ($vtfp_results, $expected_result, 'multilevel vtf forced undef (no nullkeys)');
+
+	$exit_status = $test->run(chdir => $test->curdir, args => qq[-no-absolute_program_paths -verbosity_level 0 -template_path $tdir -nullkeys mid_sp_contents $template]);
+	ok($exit_status>>8 == 0, "non-zero exit: $exit_status");
+	$vtfp_results = from_json($test->stdout);
+	$vtfp_err = $test->stderr;
+
+	$expected_result = {
+          'version' => '2.0',
+          'edges' => [],
+          'nodes' => [
+                       {
+                         'id' => 'mid_blather',
+                         'type' => 'EXEC',
+                         'use_STDIN' => 'false',
+                         'use_STDOUT' => 'true',
+                         'cmd' => [
+                                    'echo',
+                                    'TB [top SP] TB',
+                                    'MID_DFLT'
+                                  ]
+                       },
+                       {
+                         'id' => 'mid_bot_haver',
+                         'type' => 'EXEC',
+                         'use_STDIN' => 'false',
+                         'use_STDOUT' => 'true',
+                         'cmd' => [
+                                    'echo',
+                                    'TB [top SP] TB',
+                                    'MID_DFLT',
+                                    'BOTB [bot SP] BOTB'
+                                  ],
+                       }
+                     ]
+        };
+
+	is_deeply ($vtfp_results, $expected_result, 'multilevel vtf forced undef (nullkeys: mid_sp_contents)');
+};
+
 1;