| line |
true |
false |
branch |
|
44
|
1 |
9 |
unless my $activate = $args{'activate'} |
|
45
|
0 |
9 |
unless ref $activate eq "HASH" |
|
49
|
2 |
7 |
unless @act_keys == 1 and grep {/^(module|singularity|conda)$/u;} @act_keys |
|
54
|
1 |
7 |
unless $k =~ /^(queue|threads|memory|runtime)$/u |
|
60
|
1 |
5 |
unless $self->{'name'} = $args{'name'} |
|
89
|
3 |
2 |
if ($type eq 'module') { } |
|
|
1 |
1 |
elsif ($type eq 'conda') { } |
|
|
1 |
0 |
elsif ($type eq 'singularity') { } |
|
110
|
1 |
1 |
defined $img ? : |
|
121
|
1 |
5 |
if defined $args{'sample_name'} |
|
126
|
5 |
0 |
if (($inp->{'type'} // "") eq "file" and $inp->{'required'} // 0) |
|
128
|
5 |
0 |
if defined $source |
|
131
|
0 |
5 |
unless defined $source |
|
148
|
1 |
1 |
defined $args{'r1'} && defined $args{'r2'} ? : |
|
178
|
0 |
12 |
if $inp->{'slurm_sync'} |
|
182
|
1 |
11 |
if ($inp->{'required'} and not defined $val) |
|
185
|
5 |
6 |
unless defined $val |
|
188
|
1 |
5 |
if ($type eq 'file' and not -f $val) { } |
|
|
0 |
10 |
elsif ($type eq 'dir' and not -d $val) { } |
|
197
|
4 |
7 |
if $p->{'slurm_sync'} |
|
202
|
4 |
1 |
if (not defined $val and $p->{'default_env'}) |
|
207
|
0 |
7 |
if ($p->{'required'} and not defined $val) |
|
210
|
0 |
7 |
unless defined $val |
|
213
|
0 |
7 |
if ($type eq 'int' and not $val =~ /^\d+$/u) { } |
|
|
0 |
7 |
elsif ($type eq 'float' and not $val =~ /^[\d.]+$/u) { } |
|
|
0 |
7 |
elsif ($type eq 'file' and not -f $val) { } |
|
|
1 |
8 |
elsif ($type eq 'dir' and not -d $val) { } |
|
225
|
1 |
3 |
if ($self->{'outdir'}{'required'} and not defined $args{'outdir'}) |
|
264
|
0 |
2 |
unless my $sample = $args{'sample'} |
|
265
|
0 |
2 |
unless my $outdir = $args{'outdir'} |
|
278
|
5 |
0 |
if defined $cmd_args{$name} |
|
279
|
0 |
0 |
if ($p->{'default_env'} and defined $ENV{$p->{'default_env'}}) { } |
|
|
0 |
0 |
elsif (defined $p->{'default'}) { } |
|
291
|
1 |
2 |
unless $out->{'required'} |
|
309
|
2 |
0 |
$use_tmpdir ? : |
|
|
0 |
2 |
defined $args{'scratch_dir'} ? : |
|
359
|
2 |
0 |
if ($activation) |
|
377
|
2 |
0 |
if ($validation) |
|
408
|
1 |
2 |
if defined $args{$name} |
|
409
|
1 |
1 |
if ($p->{'default_env'} and defined $ENV{$p->{'default_env'}}) { } |
|
|
1 |
0 |
elsif (defined $p->{'default'}) { } |
|
419
|
1 |
4 |
unless defined $args{$name} |
|
421
|
2 |
2 |
if ($type eq "file" or $type eq "dir") |
|
427
|
1 |
0 |
if (defined $args{'outdir'}) |
|
430
|
1 |
0 |
if defined $abs |
|
440
|
1 |
0 |
if ($rt =~ /^(\d+):(\d+):(\d+)$/u) |
|
443
|
0 |
0 |
if ($rt =~ /^(\d+):(\d+)$/u) |
|
446
|
0 |
0 |
if ($rt =~ /^(\d+)$/u) |
|
454
|
0 |
0 |
if $u eq "D" |
|
455
|
0 |
0 |
if $u eq "H" |
|
456
|
0 |
0 |
if $u eq "M" |
|
457
|
0 |
0 |
if $u eq "S" |
|
491
|
2 |
1 |
unless $p->{'slurm_sync'} |
|
492
|
1 |
0 |
if ($p->{'slurm_sync'} eq 'threads') { } |
|
|
0 |
0 |
elsif ($p->{'slurm_sync'} eq 'memory') { } |
|
546
|
1 |
1 |
if defined $args{$inp->{'name'}} |
|
552
|
3 |
0 |
if defined $args{$p->{'name'}} |