Merge pull request #56 from wtsi-npg/devel

release 0.10
wtsi-npg · Nov 20, 2014 · 4999234 · 4999234
2 parents 6b33edc + 9c63110
commit 4999234
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Showing 17 changed files with 761 additions and 346 deletions.
diff --git a/bin/viv.pl b/bin/viv.pl
@@ -99,7 +99,7 @@
 		if($to_node->{type} eq q[EXEC]) {
 			$data_xfer_name = _create_fifo($edge->{from});
 		}
-		elsif($to_node->{subtype} eq q[DUMMY]) {
+		elsif(defined $to_node->{subtype} and $to_node->{subtype} eq q[DUMMY]) {
 			$data_xfer_name = q[];
 		}
 		else {
@@ -126,7 +126,9 @@
 # kick off any unblocked EXEC nodes, noting their details for later release of any dependants
 my %pid2id = ();
 for my $node_id (keys %exec_nodes) {
-	if($exec_nodes{$node_id}->{wait_counter} == 0 and not $exec_nodes{$node_id}->{pid}) { # green light - execute
+	my $wait_counter = $exec_nodes{$node_id}->{wait_counter};
+	$wait_counter ||= 0;
+	if($wait_counter == 0 and not $exec_nodes{$node_id}->{pid}) { # green light - execute
 
 		my $node = $exec_nodes{$node_id};
 		if((my $pid=_fork_off($node, $do_exec))) {
@@ -176,7 +178,7 @@
 	}else{
 
 		$logger->($VLMED, sprintf(q[Child %s (pid: %d), return_status: %#04X, wifexited: %d (%#04X), wexitstatus: %s], $completed_node->{id}, $pid, $status, $wifexited, $wexitstatus, $wexitstatus), "\n");
-		$logger->($VLMED, sprintf(q[Child %s (pid: %d), wifsignaled: %#04X, wtermsig: %s], $completed_node->{id}, $pid, $wifsignaled, $wtermsig), "\n");
+		$logger->($VLMED, sprintf(q[Child %s (pid: %d), wifsignaled: %#04X, wtermsig: %s], $completed_node->{id}, $pid, $wifsignaled, ($wifsignaled? $wtermsig: q{NA})), "\n");
 		$logger->($VLMED, sprintf(q[Child %s (pid: %d), wifexited: %#04X, wexitstatus: %s], $completed_node->{id}, $pid, $wifexited, $wexitstatus), "\n");
 
 		if($dependants_list and @$dependants_list) {

diff --git a/bin/vtfp.pl b/bin/vtfp.pl
@@ -281,7 +281,7 @@ sub do_substitutions {
 		my $subst_value = make_substitutions($subst_param_name, $substitutable_params, \%subst_requests, $query_mode);
 
 		if($query_mode) {
-			print $out join(qq[\t], ($subst_param_name, ($substitutable_params->{$subst_param_name}->{required}? q[required]: q[not_required]), $substitutable_params->{$subst_param_name}->{parent_id}, $substitutable_params->{$subst_param_name,}->{attrib_name}, )), "\n";
+			print $out join(qq[\t], ($subst_param_name, ($substitutable_params->{$subst_param_name}->{required}? q[required]: q[not_required]), $substitutable_params->{$subst_param_name}->{parent_id}, $substitutable_params->{$subst_param_name}->{attrib_name}, )), "\n";
 		}
 	}
 
@@ -380,23 +380,20 @@ sub resolve_subst_to_string {
 
 	if(not defined $subst_value) {
 		# do a little unpacking for readability
-		my $attrib_name = $subst_param->{attrib_name};
-		my $elem_index = $subst_param->{elem_index};
-		$attrib_name ||= "element $elem_index";
 		my $subst_param_name = $subst_param->{param_name};
 		my $parent_id = $subst_param->{parent_id};
 		$parent_id ||= q[NO_PARENT_ID];   # should be ARRAY?
 
 		if($subst_param->{required} and not $query_mode) { # required means "must be specified by the caller", so default value is disregarded
 #			$logger->($VLFATAL, q[No substitution specified for required substitutable param (], $subst_param_name, q[ for ], $attrib_name, q[ in ], $parent_id, q[) - use -q for full list of substitutable parameters]);
 			# NOTE: the decision to fail can only be decided at the top level of the subst_param structure
-			$logger->($VLMIN, q[No substitution specified for required substitutable param ], $subst_param_name, q[ for ], $attrib_name, q[ in ], $parent_id);
+			$logger->($VLMIN, q[No substitution specified for required substitutable param ], $subst_param_name);
 			return;
 		}
 
 		$subst_value = $subst_param->{default_value};
 		if(not defined $subst_value) {
-			$logger->($VLMIN, q[No default value specified for apparent substitutable param (], $subst_param_name, q[ for ], $attrib_name, q[ in ], $parent_id, q[)]);
+			$logger->($VLMIN, q[No default value specified for apparent substitutable param ], $subst_param_name);
 		}
 	}
 
@@ -422,10 +419,8 @@ sub resolve_subst_array {
 	my ($subst_param, $subst_value, $query_mode) = @_;
 
 	if(ref $subst_value ne q[ARRAY]) {
-		$logger->($VLMIN, q[Attempt to substitute array for non-array in substitutable param (],
-				$subst_param->{param_name},
-				q[ for ], $subst_param->{attrib_name},
-				q[ in ], ($subst_param->{parent_id}? $subst_param->{parent_id}: q[UNNAMED_PARENT]), q[)]);
+		$logger->($VLMIN, q[Attempt to substitute array for non-array in substitutable param ],
+				$subst_param->{param_name});
 		return;
 	}
 
@@ -440,17 +435,12 @@ sub resolve_subst_array {
 		}
 		else {
 			if($subst_param->{required}) {
-				$logger->($VLFATAL, q[No substitution specified for required substitutable param (],
-						$subst_param->{param_name},
-						q[ for ], $subst_param->{attrib_name},
-						q[ in ], ($subst_param->{parent_id}? $subst_param->{parent_id}: q[UNNAMED_PARENT]),
-						q[) - use -q for full list of substitutable parameters]);
+				$logger->($VLFATAL, q[No substitution specified for required substitutable param ],
+						$subst_param->{param_name});
 			}
 			else {
-				$logger->($VLMIN, q[No default value specified for apparent substitutable param (],
-						$subst_param->{param_name},
-						q[ for ], $subst_param->{attrib_name},
-						q[ in ], ($subst_param->{parent_id}? $subst_param->{parent_id}: q[UNNAMED_PARENT]), q[)]);
+				$logger->($VLMIN, q[No default value specified for apparent substitutable param ],
+						$subst_param->{param_name});
 				return;
 			}
 		}

diff --git a/data/bcl2bam_phix_deplex_wtsi_stage1_template.vtf b/data/bcl2bam_phix_deplex_wtsi_stage1_template.vtf
@@ -218,7 +218,7 @@
 	{
 		"id":"prefilter",
 		"type":"EXEC",
-		"cmd":"/nfs/users/nfs_j/js10/teepot-1.0.1/teepot -m2M __PF1__ __PF2__"
+		"cmd":"teepot -m2M __PF1__ __PF2__"
 	},
 
 	{
@@ -250,13 +250,13 @@
 	{
 		"id":"tee_split",
 		"type":"EXEC",
-		"cmd":"mbuffer -f -q -m 5M -o __PIPE1__ -o __PIPE2__"
+		"cmd":"teepot -m 5M __FILTERED_BAM_OUT__ __SPLIT_BAM_OUT__"
 	},
 
 	{
 		"id":"tee_decode",
 		"type":"EXEC",
-		"cmd":"/nfs/users/nfs_j/js10/teepot-1.0.1/teepot -m2M __TD1__ __TD2__"
+		"cmd":"teepot -m2M __TD1__ __TD2__"
 	},
 
 	{
@@ -401,13 +401,13 @@
 
 	{
 		"id":"tee_to_filtered_bam",
-		"from":"tee_split:__PIPE1__",
+		"from":"tee_split:__FILTERED_BAM_OUT__",
 		"to":"filtered_bam"
 	},
 
 	{
 		"id":"tee_to_sort",
-		"from":"tee_split:__PIPE2__",
+		"from":"tee_split:__SPLIT_BAM_OUT__",
 		"to":"splitter"
 	}
 

diff --git a/data/bwamem_wtsi_stage2_template.vtf b/data/bwamem_wtsi_stage2_template.vtf
@@ -1,5 +1,5 @@
 {
-"description":"Process DNA seq data in BAM files within NPG Pipeline producing WTSI DNAP Sequencing Informatics BAM output: full PG history, complete SQ lines, adapter marking, recoding indexing sequence etc",
+"description":"Process DNA seq data in BAM files within second stage of NPG Pipeline producing WTSI DNAP Sequencing Informatics output",
 "nodes":[
 	{
 		"id":"bmd_phix_multiway",
@@ -316,7 +316,7 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":"teepot -w 300 -m 1G __OUT1__ __OUT2__"
+		"cmd":"teepot -w 300 -m 1G __PHIX_ALN_OUT__ __TGT_ALN_OUT__"
 	},
 	{
 		"id":"bamrecompress_input",
@@ -549,14 +549,15 @@
 	},
 	{
 		"id":"bammarkduplicates_phix",
+		"comment":"default tool bamstreamingmarkduplicates must be from Biobambam >= 0.0.174",
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
 		"cmd":{"subst_param_name":"bammarkduplicates_phix",
 			"required":"yes",
 			"subst_constructor":{
 				"vals":[
-					{"subst_param_name":"bmd_cmd","required":"no","default":"bammarkduplicates2"},
+					{"subst_param_name":"bmd_cmd","required":"no","default":"bamstreamingmarkduplicates"},
 					" level=0 ",
 					"verbose=0 ",
 					"M=",
@@ -620,14 +621,15 @@
 	},
 	{
 		"id":"bammarkduplicates_target",
+		"comment":"default tool bamstreamingmarkduplicates must be from Biobambam >= 0.0.174",
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
 		"cmd":{"subst_param_name":"bammarkduplicates_target",
 			"required":"yes",
 			"subst_constructor":{
 				"vals":[
-					{"subst_param_name":"bmd_cmd","required":"no","default":"bammarkduplicates2"},
+					{"subst_param_name":"bmd_cmd","required":"no","default":"bamstreamingmarkduplicates"},
 					" level=0 ",
 					"verbose=0 ",
 					"M=",
@@ -824,7 +826,7 @@
 	},
 	{
 		"id":"ti_to_brc",
-		"from":"tee_input:__OUT1__",
+		"from":"tee_input:__PHIX_ALN_OUT__",
 		"to":"bamrecompress_input"
 	},
 	{
@@ -834,7 +836,7 @@
 	},
 	{
 		"id":"ti_to_bamcollate2_ranking",
-		"from":"tee_input:__OUT2__",
+		"from":"tee_input:__TGT_ALN_OUT__",
 		"to":"bamcollate2_ranking"
 	},
 	{

diff --git a/data/snap_sample_template.vtf b/data/snap_sample_template.vtf
@@ -411,7 +411,7 @@
 	{
 		"id":"tee_headerSQfix",
 		"type":"EXEC",
-		"cmd":"mbuffer -f -q -m 5M -o - -o __OUT1__",
+		"cmd":"teepot -m 5M __HEADER_FIX_OUT__ __FULL_BAM_OUT__",
 		"comment":"get deadlock when tee used here"
 	},
 	{
@@ -429,7 +429,7 @@
 	{
 		"id":"mbuffer_headerSQfix",
 		"type":"EXEC",
-		"cmd":"mbuffer -f -q -m 5M"
+		"cmd":"teepot -m 5M -"
 	},
 	{
 		"id":"reheader_headerSQfix",
@@ -785,7 +785,7 @@
 	},
 	{
 		"id":"tee_headerSQfix_to_sam",
-		"from":"tee_headerSQfix:__OUT1__",
+		"from":"tee_headerSQfix:__HEADER_FIX_OUT__",
 		"to":"sam_headerSQfix"
 	},
 	{
@@ -805,7 +805,7 @@
 	},
 	{
 		"id":"tee_headerSQfix_to_mbuffer",
-		"from":"tee_headerSQfix",
+		"from":"tee_headerSQfix:__FULL_BAM_OUT__",
 		"to":"mbuffer_headerSQfix"
 	},
 	{

diff --git a/data/tophat2_wtsi_stage2_template.vtf b/data/tophat2_wtsi_stage2_template.vtf
@@ -1,5 +1,5 @@
 {
-"description":"Process RNASeq data in BAM files within NPG Pipeline producing WTSI DNAP Sequencing Informatics BAM output: full PG history, complete SQ lines, adapter marking, recoding indexing sequence etc",
+"description":"Process RNASeq data in BAM files within second stage of NPG Pipeline producing WTSI DNAP Sequencing Informatics output",
 "nodes":[
 	{
 		"id":"bmd_phix_multiway",
@@ -314,8 +314,8 @@
 		"id":"tee_input",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"tee __FIFO__"
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 -m 1G __PHIX_ALN_OUT__ __TGT_ALN_OUT__"
 	},
 	{
 		"id":"bamrecompress_input",
@@ -651,8 +651,8 @@
 		"id":"tee_headerSQfix",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"mbuffer -f -q -m 5M -o - -o __OUT1__",
+		"use_STDOUT": false,
+		"cmd":"teepot -m 5M __HEADER_FIX_OUT__ __FULL_BAM_OUT__",
 		"comment":"get deadlock when tee used here"
 	},
 	{
@@ -676,7 +676,7 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
-		"cmd":"mbuffer -f -q -m 5M"
+		"cmd":"teepot -m 5M -"
 	},
 	{
 		"id":"reheader_headerSQfix",
@@ -785,14 +785,15 @@
 	},
 	{
 		"id":"bammarkduplicates_phix",
+		"comment":"default tool bamstreamingmarkduplicates must be from Biobambam >= 0.0.174",
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
 		"cmd":{"subst_param_name":"bammarkduplicates_phix",
 			"required":"yes",
 			"subst_constructor":{
 				"vals":[
-					{"subst_param_name":"bmd_cmd","required":"no","default":"bammarkduplicates2"},
+					{"subst_param_name":"bmd_cmd","required":"no","default":"bamstreamingmarkduplicates"},
 					" level=0 ",
 					"M=",
 					{"subst_param_name":"outdatadir","required":"no","default":"."},
@@ -855,14 +856,15 @@
 	},
 	{
 		"id":"bammarkduplicates_target",
+		"comment":"default tool bamstreamingmarkduplicates must be from Biobambam >= 0.0.174",
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
 		"cmd":{"subst_param_name":"bammarkduplicates_target",
 			"required":"yes",
 			"subst_constructor":{
 				"vals":[
-					{"subst_param_name":"bmd_cmd","required":"no","default":"bammarkduplicates2"},
+					{"subst_param_name":"bmd_cmd","required":"no","default":"bamstreamingmarkduplicates"},
 					" level=0 ",
 					"M=",
 					{"subst_param_name":"outdatadir","required":"no","default":"."},
@@ -1058,7 +1060,7 @@
 	},
 	{
 		"id":"ti_to_brc",
-		"from":"tee_input",
+		"from":"tee_input:__PHIX_ALN_OUT__",
 		"to":"bamrecompress_input"
 	},
 	{
@@ -1068,7 +1070,7 @@
 	},
 	{
 		"id":"ti_to_bamcollate2_ranking",
-		"from":"tee_input:__FIFO__",
+		"from":"tee_input:__TGT_ALN_OUT__",
 		"to":"bamcollate2_ranking"
 	},
 	{
@@ -1133,7 +1135,7 @@
 	},
 	{
 		"id":"tee_headerSQfix_to_sam",
-		"from":"tee_headerSQfix:__OUT1__",
+		"from":"tee_headerSQfix:__HEADER_FIX_OUT__",
 		"to":"sam_headerSQfix"
 	},
 	{
@@ -1153,7 +1155,7 @@
 	},
 	{
 		"id":"tee_headerSQfix_to_mbuffer",
-		"from":"tee_headerSQfix",
+		"from":"tee_headerSQfix:__FULL_BAM_OUT__",
 		"to":"mbuffer_headerSQfix"
 	},
 	{

diff --git a/data/vtlib/README.vtlib b/data/vtlib/README.vtlib
@@ -10,8 +10,7 @@ $ vtfp.pl -l aln_vtf.log -o aln.json \
 -keys alignment_method -vals <ALIGNMENT_TEMPLATE_JSON> \
 -keys reposdir -vals <REFERENCE_REPOSITORY_ROOT> \
 -keys alignment_reference_genome_name -vals <PATH_TO_ALIGNER_REFERENCE_FROM_ROOT> \
--keys picard_reference_dict_name -vals <PATH_TO_PICARD_DICT_TARGET_REFERENCE_FROM_ROOT> \
--keys picard_dict_name_phix -vals <PATH_TO_PICARD_DICT_PHIX_REFERENCE_FROM_ROOT> \
+-keys reference_dict_name -vals <PATH_TO_PICARD_DICT_TARGET_REFERENCE_FROM_ROOT> \
 -keys reference_genome_fasta_name -vals <PATH_TO_FASTA_REFERENCE_FROM_ROOT> \
 -keys phix_reference_genome_fasta_name -vals <PATH_TO_FASTA_PHIX_REFERENCE_FROM_ROOT> \
 -keys aligner_numthreads -vals <NUMBER_OF_THREADS_USED_BY_ALIGNER> \
@@ -28,22 +27,21 @@ $ viv.pl -x -s -o v 3 -o viv_run.log aln.json
  alignment_method - the name of the template file containing the alignment steps (without the ".json" suffix)
  repos_dir - root of the reference repository, useful for when the various reference formats appear in a common location
  alignment_reference_genome_name - path from the repos_dir to the reference needed by the selected aligner
- picard_reference_dict_name - picard reference_dict for target, used to reconstruct bam header SQ lines after alignment
- picard_dict_name_phix - picard reference_dict for phix, used to reconstruct bam header SQ lines after alignment
+ reference_dict_name - picard reference_dict for target, used to reconstruct bam header SQ lines after alignment
  reference_genome_fasta_name - path from reposdir to fasta reference for target, used by scramble to create cram files
  phix_reference_genome_fasta_name - path from reposdir to fasta reference for phix, used by scramble to create cram files
  aligner_numthreads - number of threads used bny the aligner, for aligners which have this feature
 
 
 Examples:
 bwa aln:
-$ vtfp.pl -l was2_bwa_aln.vtf.log -o was2_bwa_aln.json -keys indatadir -vals indata -keys outdatadir -vals outdata_bwa_aln -keys cfgdatadir -vals cfgdata -keys tmpdir -vals tmpdata -keys rpt -vals 13430_8#1 -keys alignment_method -vals bwa_aln -keys reposdir -vals /paths/to/references -keys alignment_reference_genome_name -vals Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa -keys picard_reference_dict_name -vals Homo_sapiens/1000Genomes_hs37d5/all/picard/hs37d5.fa.dict -keys picard_dict_name_phix -vals PhiX/default/all/picard/phix_unsnipped_short_no_N.fa.dict -keys reference_genome_fasta_name -vals Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa -keys phix_reference_genome_fasta_name -vals PhiX/default/all/fasta/phix_unsnipped_short_no_N.fa -keys aligner_numthreads -vals 8 cfgdata/alignment_wtsi_stage2_template.json 
+$ vtfp.pl -l aws2_bwa_aln.vtf.log -o aws2_bwa_aln.json -keys indatadir -vals indata -keys outdatadir -vals outdata_bwa_aln -keys cfgdatadir -vals cfgdata -keys tmpdir -vals tmpdata -keys rpt -vals 13430_8#1 -keys alignment_method -vals bwa_aln -keys reposdir -vals /paths/to/references -keys alignment_reference_genome_name -vals Homo_sapiens/1000Genomes_hs37d5/all/bwa/hs37d5.fa -keys reference_dict_name -vals Homo_sapiens/1000Genomes_hs37d5/all/picard/hs37d5.fa.dict -keys reference_genome_fasta_name -vals Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa -keys phix_reference_genome_fasta_name -vals PhiX/default/all/fasta/phix_unsnipped_short_no_N.fa -keys aligner_numthreads -vals 8 cfgdata/alignment_wtsi_stage2_template.json 
 
 bwa mem:
-$ vtfp.pl -l was2_bwa_mem.vtf.log -o was2_bwa_mem.json -keys indatadir -vals indata -keys outdatadir -vals outdata_bwa_mem -keys cfgdatadir -vals cfgdata -keys tmpdir -vals tmpdata -keys rpt -vals 13430_8#1 -keys alignment_method -vals bwa_mem -keys reposdir -vals /path/to/references -keys alignment_reference_genome_name -vals Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa -keys picard_reference_dict_name -vals Homo_sapiens/1000Genomes_hs37d5/all/picard/hs37d5.fa.dict -keys picard_dict_name_phix -vals PhiX/default/all/picard/phix_unsnipped_short_no_N.fa.dict -keys reference_genome_fasta_name -vals Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa -keys phix_reference_genome_fasta_name -vals PhiX/default/all/fasta/phix_unsnipped_short_no_N.fa -keys aligner_numthreads -vals 8 cfgdata/alignment_wtsi_stage2_template.json
+$ vtfp.pl -l aws2_bwa_mem.vtf.log -o aws2_bwa_mem.json -keys indatadir -vals indata -keys outdatadir -vals outdata_bwa_mem -keys cfgdatadir -vals cfgdata -keys tmpdir -vals tmpdata -keys rpt -vals 13430_8#1 -keys alignment_method -vals bwa_mem -keys reposdir -vals /path/to/references -keys alignment_reference_genome_name -vals Homo_sapiens/1000Genomes_hs37d5/all/bwa0_6/hs37d5.fa -keys reference_dict_name -vals Homo_sapiens/1000Genomes_hs37d5/all/picard/hs37d5.fa.dict -keys reference_genome_fasta_name -vals Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa -keys phix_reference_genome_fasta_name -vals PhiX/default/all/fasta/phix_unsnipped_short_no_N.fa -keys aligner_numthreads -vals 8 cfgdata/alignment_wtsi_stage2_template.json
 
 tophat2:
-$ vtfp.pl -l was2_tophat2.vtf.log -o was2_tophat2.json -keys indatadir -vals indata -keys outdatadir -vals outdata_tophat2 -keys cfgdatadir -vals cfgdata -keys tmpdir -vals tmpdata -keys rpt -vals 13430_8#1 -keys alignment_method -vals tophat2 -keys reposdir -vals /path/to/references -keys alignment_reference_genome_name -vals Homo_sapiens/1000Genomes_hs37d5/all/bowtie2/hs37d5.fa -keys picard_reference_dict_name -vals Homo_sapiens/1000Genomes_hs37d5/all/picard/hs37d5.fa.dict -keys picard_dict_name_phix -vals PhiX/default/all/picard/phix_unsnipped_short_no_N.fa.dict -keys reference_genome_fasta_name -vals Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa -keys phix_reference_genome_fasta_name -vals PhiX/default/all/fasta/phix_unsnipped_short_no_N.fa -keys aligner_numthreads -vals 8 cfgdata/alignment_wtsi_stage2_template.json
+$ vtfp.pl -l aws2_tophat2.vtf.log -o aws2_tophat2.json -keys indatadir -vals indata -keys outdatadir -vals outdata_tophat2 -keys cfgdatadir -vals cfgdata -keys tmpdir -vals tmpdata -keys rpt -vals 13430_8#1 -keys alignment_method -vals tophat2 -keys reposdir -vals /path/to/references -keys alignment_reference_genome_name -vals Homo_sapiens/1000Genomes_hs37d5/all/bowtie2/hs37d5.fa -keys reference_dict_name -vals Homo_sapiens/1000Genomes_hs37d5/all/picard/hs37d5.fa.dict -keys reference_genome_fasta_name -vals Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa -keys phix_reference_genome_fasta_name -vals PhiX/default/all/fasta/phix_unsnipped_short_no_N.fa -keys aligner_numthreads -vals 8 cfgdata/alignment_wtsi_stage2_template.json