Do not require manual maintenance of module names that finalize depen…

…ds on

lib/HMF/Pipeline/Config.pm

@@ -203,21 +203,10 @@ sub sampleControlBamsAndJobs {
 sub allRunningJobs {
     my ($opt) = @_;
 
-    # is this split into modules actually required anywhere?
-    # surely better to use *all* keys instead of a hard-coded list?
-    my @running_jobs = uniq grep { defined } map { @$_ } grep { defined } @{$opt->{RUNNING_JOBS}}{
-        # flatten registered jobs into one list
-        "baf",
-        "prestats",
-        sort keys %{$opt->{SAMPLES}},
-        "slicing",
-        "poststats",
-        "somvar",
-        "cnv",
-        "sv",
-        "kinship",
-    };
-    return \@running_jobs;
+    my @running_job_chains = grep { defined } values %{$opt->{RUNNING_JOBS}};
+    my @running_jobs = map { @$_ } @running_job_chains;
+    my @unique_jobs = uniq sort grep { defined } @running_jobs;
+    return \@unique_jobs;
 }
 
 sub recordGitVersion {

t/03-config.t

@@ -290,9 +290,18 @@ is_deeply([ sampleBamAndJobs("b", $opt) ], [ "$temp_dir/b/mapping/b.bam", [ "job
 is_deeply([ sampleBamAndJobs("c", $opt) ], [ "$temp_dir/c/mapping/c.bam", undef ], "bam path and no jobs for sample c"); # should return empty list?
 is_deeply([ sampleBamsAndJobs($opt) ], [ {a => "$temp_dir/a/mapping/a.bam", b => "$temp_dir/b/mapping/b.bam"}, [ "job1", "job2", "joba", "jobb" ] ], "bam paths and jobs for samples");
 
-# not really clear how to test this - allRunningJobs should probably not hard-code keys
-$opt->{RUNNING_JOBS}->{somvar} = [ "fb", "vs" ];
-is_deeply(allRunningJobs($opt), [ "job1", "job2", "joba", "jobb", "fb", "vs" ], "'all' running jobs");
+
+is_deeply(allRunningJobs({RUNNING_JOBS => {}}), [], "no running jobs");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => undef}}), [], "no skipped job chains");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => []}}), [], "no skipped job chains");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => ["job"]}}), ["job"], "single job chain");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => [ "job1", "job2" ]}}), [ "job1", "job2" ], "multiple job chain");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => undef, b => ["job"]}}), ["job"], "job chain after skipped job chain");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => ["job1"], b => ["job2"]}}), [ "job1", "job2" ], "multiple job chains");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => [undef]}}), [], "skipped job within chain");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => [ undef, "job" ]}}), ["job"], "job after skipped job within chain");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => [ "job", "job" ]}}), ["job"], "unique job within chain");
+is_deeply(allRunningJobs({RUNNING_JOBS => {a => ["job"], b => ["job"]}}), ["job"], "unique job across chains");
 
 
 my $metadata_path = catfile($temp_dir, "metadata");