| line |
true |
false |
branch |
|
718
|
0 |
6 |
unless $self->verbose
|
|
720
|
3 |
3 |
if ($type eq 'start') { }
|
|
|
3 |
0 |
elsif ($type eq 'end') { }
|
|
730
|
0 |
45 |
unless $k
|
|
769
|
0 |
6 |
unless exists $self->yaml->{'global'}
|
|
788
|
15 |
0 |
unless $self->save_object_env
|
|
817
|
0 |
99 |
unless $self->create_outdir
|
|
819
|
0 |
99 |
if ($self->{'outdir'} =~ /\{\$/)
|
|
822
|
35 |
64 |
if not -d $self->outdir
|
|
851
|
0 |
6 |
if ($self->has_samples and not $self->resample)
|
|
859
|
2 |
4 |
if ($self->find_by_dir) { }
|
|
888
|
6 |
0 |
if ($self->verbose)
|
|
922
|
6 |
0 |
unless $self->yaml->{'plugins'}
|
|
940
|
6 |
0 |
unless $self->yaml->{'use'}
|
|
991
|
3 |
217 |
unless (exists $seen{$k})
|
|
992
|
1 |
2 |
if ($k =~ /_dir$/) { }
|
|
993
|
1 |
0 |
if ($self->coerce_paths) { }
|
|
1026
|
220 |
0 |
if defined $v
|
|
1039
|
0 |
899 |
unless $k
|
|
1041
|
180 |
719 |
unless $v
|
|
1045
|
545 |
174 |
if ($sample) { }
|
|
1057
|
60 |
0 |
if $self->create_outdir
|
|
1067
|
0 |
0 |
unless $v
|
|
1078
|
0 |
3 |
if ($self->min) { }
|
|
|
0 |
3 |
elsif ($self->sample_based) { }
|
|
|
3 |
0 |
elsif ($self->rule_based) { }
|
|
1102
|
0 |
0 |
unless open my $fh, '>', 'run-workflow.sh'
|
|
1127
|
0 |
3 |
unless $process
|
|
1130
|
0 |
9 |
unless $p
|
|
1131
|
0 |
9 |
if ($self->number_rules)
|
|
1153
|
0 |
9 |
if ($self->has_select_rules) { }
|
|
|
0 |
9 |
elsif ($self->has_match_rules) { }
|
|
1155
|
0 |
0 |
unless ($self->filter_select_rules(sub {
/^$p$/;
}
))
|
|
1160
|
0 |
0 |
if $self->auto_name
|
|
1167
|
0 |
0 |
unless ($self->map_match_rules(sub {
$p =~ /$_/;
}
))
|
|
1172
|
0 |
0 |
if $self->auto_name
|
|
1188
|
9 |
0 |
if $self->auto_name
|
|
1201
|
0 |
9 |
if ($#keys > 0) { }
|
|
|
0 |
9 |
elsif (not @keys) { }
|
|
1212
|
0 |
9 |
if (not exists $self->local_rule->{$self->key}{'process'})
|
|
1242
|
9 |
0 |
if ($self->auto_name)
|
|
1244
|
3 |
6 |
unless $self->by_sample_outdir
|
|
1248
|
0 |
9 |
if (exists $self->local_rule->{$self->key}{'override_process'} and $self->local_rule->{$self->key}{'override_process'} == 1) { }
|
|
1258
|
2 |
7 |
if (exists $self->local_rule->{$self->key}{'local'})
|
|
1268
|
9 |
0 |
unless $self->local_attr->exists('outdir')
|
|
1270
|
9 |
0 |
unless $self->local_attr->exists('indir')
|
|
1275
|
0 |
9 |
if $self->resample
|
|
1278
|
9 |
0 |
if ($self->auto_input)
|
|
1279
|
0 |
9 |
if $self->has_OUTPUT
|
|
1281
|
0 |
9 |
if $self->global_attr->exists('INPUT')
|
|
1300
|
0 |
156 |
unless $key
|
|
1316
|
9 |
9 |
if ($meta eq 'after_meta')
|
|
1321
|
9 |
9 |
unless $meta eq 'before_meta'
|
|
1325
|
9 |
0 |
if ($self->verbose)
|
|
1331
|
2 |
7 |
if (exists $self->local_rule->{$self->key}{'local'})
|
|
1343
|
0 |
9 |
if ($self->resample)
|
|
1374
|
9 |
0 |
if (not $self->override_process) { }
|
|
1376
|
30 |
15 |
if $self->by_sample_outdir
|
|
1391
|
9 |
0 |
if ($self->wait)
|
|
1422
|
0 |
30 |
if ($tt =~ /\{\$self/) { }
|
|
|
20 |
10 |
elsif ($self->has_pkey) { }
|
|
1448
|
0 |
9 |
if ($self->auto_input and $self->local_attr->exists('OUTPUT')) { }
|
|
1472
|
0 |
45 |
if $self->local_attr->exists('INPUT')
|
|
1474
|
0 |
45 |
if $self->local_attr->exists('OUTPUT')
|