Merge pull request #125 from wtsi-npg/devel

release 0.17.1

.travis.yml

@@ -0,0 +1,29 @@
+sudo: false
+language: perl
+perl:
+  - 5.16
+
+env:
+  global:
+    - secure: "Yaiv+tTD2FnvN2UwA9yEVIzLQMXR7yhLkuzJ9521MNM354SqKJUFtMLbQfdA7Rld5npylBSl1xfUOwjiraDBvtbjnC6PKpaz2fyR8/ycGptMjbWncxjNiSIxYelmw/JD9qu74Z2yIKzty7O4WqJ1IbP3OrQd/aTYViekibl7hIo="
+
+after_success:
+  - ./Build dist
+  - export DIST_FILE=$(ls p4-*.tar.gz)
+  - export MD5_FILE=$DIST_FILE.md5
+  - md5sum $DIST_FILE > $MD5_FILE
+  - export SHA256_FILE=$DIST_FILE.sha256
+  - shasum -a 256 $DIST_FILE > $SHA256_FILE
+
+deploy:
+  provider: releases
+  api-key: $GH_OAUTH
+  file:
+    - $DIST_FILE
+    - $MD5_FILE
+    - $SHA256_FILE
+  skip_cleanup: true
+  on:
+    perl: 5.16
+    tags: true
+    all_branches: true

Build.PL

@@ -60,8 +60,12 @@ my $builder = $class->new(
 
   'build_requires' => {
     'English'               => 0,
+  },
+  'test_requires' => {
     'Test::More'            => 0,
     'Test::Compile'         => 0,
+    'Test::Cmd'             => 0,
+    'Perl6::Slurp'          => 0,
   },
 
   'requires' => {
@@ -73,6 +77,7 @@ my $builder = $class->new(
     'File::Which'           => 0,
     'Getopt::Long'          => 0,
     'Getopt::Std'           => 0,
+    'Hash::Merge'           => 0,
     'JSON'                  => 0,
     'List::MoreUtils'       => 0,
     'POSIX'                 => 0,

Changes

@@ -1,6 +1,23 @@
 CHANGES LOG
 -----------
 
+release 0.17.1
+ - -n 1 flag added to seqchksum_merge.pl command in merge_aligned template to allow different tags in column 1
+ - scramble compression
+   - up to 7 for final output cram files
+   - down to 0 for internal bam streams
+ - port naming conventions (IN/OUT pre- and postfixes) adopted in templates and enforced in viv.pl
+ - vtfp.pl
+    improved error reporting
+    refactoring to ensure more consistent/intuitive evaluation of parameter values
+    allow specification of "local" parameter substitution (within a specific vtnode)
+    added --param_vals --export_param_vals flags
+    subst directive attributes ifnull and required added
+    remove dead code, review relevance of comments, general tidying
+    more tests
+ - add tests for viv.pl
+ - add (secondary stage) extra split template - remove human and another genome
+
 release 0.17
  - human split with no target align (secondary stage) template introduced
  - initial work for stage one (bcl, adapter, phiX and spatial filter to split processing) using templates

MANIFEST

@@ -2,6 +2,34 @@ bin/viv.pl
 bin/vtfp.pl
 Build.PL
 Changes
+data/bcl2bam_phix_deplex_wtsi_stage1_template.vtf
+data/bwa_post_proc.vtf
+data/hiseqx.vtf
+data/post_alignment.vtf
+data/vtlib/alignment_common.json
+data/vtlib/alignment_wtsi_stage2_humansplit_notargetalign_template.json
+data/vtlib/alignment_wtsi_stage2_humansplit_template.json
+data/vtlib/alignment_wtsi_stage2_template.json
+data/vtlib/auxmerge_prep.json
+data/vtlib/auxmerge_prep_realign.json
+data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json
+data/vtlib/bwa_aln_alignment.json
+data/vtlib/bwa_aln_se_alignment.json
+data/vtlib/bwa_mem_alignment.json
+data/vtlib/final_output_noalign_prep.json
+data/vtlib/final_output_prep.json
+data/vtlib/merge_aligned.json
+data/vtlib/merge_final_output_prep.json
+data/vtlib/post_alignment.json
+data/vtlib/pre_alignment.json
+data/vtlib/pre_alignment_realign.json
+data/vtlib/README.vtlib
+data/vtlib/realignment_wtsi_template.json
+data/vtlib/seqchksum.json
+data/vtlib/seqchksum_hs.json
+data/vtlib/seqchksum_realign.json
+data/vtlib/split_by_chromosome.json
+data/vtlib/tophat2_alignment.json
 examples/bwa_aln_cfg.png
 examples/bwa_mem/bwa_mem_alignment.vtf
 examples/bwa_mem/generic_alignment_with_phix.vtf
@@ -18,12 +46,22 @@ examples/tophat2_cfg.png
 MANIFEST			This list of files
 README
 README.vtfp
-t/data/simple_failing_pipeline.vtf
-t/data/simple_pipeline.vtf
 t/00-scripts_compile.t
+t/10-vtfp-array_expansion.t
+t/10-vtfp-param_ring.t
+t/10-vtfp-pv.t
+t/10-vtfp-subst_directive.t
+t/data/10-vtfp-array_expansion.json
+t/data/10-vtfp-param_ring.json
+t/data/10-vtfp-pv.json
 visualisation/bwa_aln.cfg
 visualisation/bwa_aln.json
+visualisation/cgi-bin/getProgress
 visualisation/config_view.html
+visualisation/edit.html
+visualisation/p4_edit.css
+visualisation/p4_edit.js
 visualisation/README.visualisation
 visualisation/tophat2.cfg
 visualisation/tophat2.json
+visualisation/view.js

bin/viv.pl

@@ -240,7 +240,7 @@ sub _update_node_data_xfer {
 				#ensure port is connected to in manner suggested by naming convention
 				croak 'Node '.($node->{'id'})." port $port connected as ".($edge_side == $FROM?q("from"):q("to")) if (($inout eq q(OUT))^($edge_side == $FROM));
 			} else {
-				$logger->($VLMED, 'Node '.($node->{'id'})." has poorly described port $port (no _{IN,OUT}__ {suf,pre}fix)\n");
+				croak 'Node '.($node->{'id'})." has poorly described port $port (no _{IN,OUT}__ {suf,pre}fix)\n";
 			}
 			my $cmd = $node->{'cmd'};
 			for my$cmd_part ( ref $cmd eq 'ARRAY' ? @{$cmd}[1..$#{$cmd}] : ($node->{'cmd'}) ){