ApiCommonWorkflow/Main/lib/perl/WorkflowSteps/MakeArrayProbeMappingNextflowConfig.pm at 661b6f12d5fc846a6d9c5f3f59f24a7005e6eeb8 · VEuPathDB/ApiCommonWorkflow · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
package ApiCommonWorkflow::Main::WorkflowSteps::MakeArrayProbeMappingNextflowConfig;

@ISA = (ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep);

use strict;
use ApiCommonWorkflow::Main::WorkflowSteps::WorkflowStep;

sub run {
  my ($self, $test, $undo) = @_;

  my $gtfFeatureType = "exon";
  my $geneGtfTag = "gene_id";
  my $minProbes = 1;


  my $resultsDirectory = $self->getParamValue("resultsDirectory");

  my $platformType = $self->getParamValue("platformType");
  my $projectName = $self->getParamValue("projectName");

  #my $wantSplicedAlignments = lc $self->getParamValue("wantSplicedAlignments");
  my $wantSplicedAlignments = "true";
  if($platformType ne 'expression' || $projectName eq 'TriTrypDB' || $projectName eq 'HostDB') {
    $wantSplicedAlignments = "false";
  }

  my $gtfFile = $self->getParamValue("gtfFile");
  my $genomeFile = $self->getParamValue("genomeFile");
  my $finalDirectory = $self->getParamValue("finalDirectory");
  my $nextflowConfigFile = $self->getParamValue("nextflowConfigFile");
  my $organismAbbrev = $self->getParamValue("organismAbbrev");

  my $outputFileName = $self->getParamValue("outputFileName");
  my $inputProbesFastaName = $self->getParamValue("inputProbesFastaName");


  my $makeCdfFile = lc $self->getParamValue("makeCdfFile");
  my $makeNdfFile = lc $self->getParamValue("makeNdfFile");
  my $geneProbeMappingFileName = $self->getParamValue("geneProbeMappingFileName");

  # defaults for non cdf/ndf mapping
  my $vendorMappingFileName = "NA";
  my $probeRows = 0;
  my $probeCols = 0;

  if($self->getBooleanParamValue("makeCdfFile") || $self->getBooleanParamValue("makeNdfFile")) {
      $vendorMappingFileName = $self->getParamValue("vendorMappingFileName");
  }

  if($self->getBooleanParamValue("makeCdfFile")) {
      $probeRows = $self->getParamValue("probeRows");
      $probeCols = $self->getParamValue("probeCols");
  }

  my $limitNU = $self->getParamValue("limitNU");

  # DEPRECATED?? (these are configured but not used??)
  my $variableLengthReads = lc $self->getParamValue("variableLengthReads");
  my $numInsertions = $self->getParamValue("numInsertions");

  my $workflowDataDir = $self->getWorkflowDataDir();

  my $workingDirRelativePath = $self->getParamValue("workingDirRelativePath");
  my $digestedGtfFilePath = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $gtfFile);
  my $digestedGenomeFilePath = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $genomeFile);
  my $digestedOutputDir = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $resultsDirectory);
  my $digestedFinalDir = $self->relativePathToNextflowClusterPath($workingDirRelativePath, $finalDirectory);


  my $clusterServer = $self->getSharedConfig('clusterServer');
  my $clusterWorkflowDataDir = $self->getClusterWorkflowDataDir();
  my $executor = $self->getClusterExecutor();
  my $lsfEnv = $self->getNextflowLsfScratchEnvBlock();

  my $clusterConfigFile = "\$baseDir/conf/${executor}.config";

  if ($undo) {
      $self->runCmd(0, "rm $workflowDataDir/$nextflowConfigFile");
  } else {
      my $nextflowConfig = "$workflowDataDir/$nextflowConfigFile";
      open(F, ">$nextflowConfig") || die "Can't open task prop file '$nextflowConfig' for writing";

      my $configString = <<NEXTFLOW;
params {
  genomeFastaFile = "$digestedGenomeFilePath"
  outputDir = "$digestedOutputDir"
  outputFileName = "$outputFileName"
  probesFastaFile = "$digestedFinalDir/$inputProbesFastaName"
  wantSplicedAlignments = $wantSplicedAlignments
  platformType = "$platformType"
  gtfFile = "$digestedGtfFilePath"
  makeCdfFile = $makeCdfFile
  makeNdfFile = $makeNdfFile
  outputMappingFileName = "$geneProbeMappingFileName"
  vendorMappingFile = "$digestedFinalDir/$vendorMappingFileName"
  arrayRows = $probeRows
  arrayColumns = $probeCols
}

process {
  maxForks = 1

  withName: gsnapMapping {
    ext.nPaths = 30
    ext.params = "-n $limitNU -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 -I 0 -X 1000 -f"
  }

  withName: bedToGene2Probe {
    ext.gtfFeatureType = "$gtfFeatureType"
    ext.geneGtfTag = "$geneGtfTag"
  }

  withName: cdfFromGene2Probe {
    ext.minProbes = $minProbes
  }
}

includeConfig "$clusterConfigFile"

NEXTFLOW

      print F $configString . $lsfEnv;
      close(F);
  }
}

1;