Fixes missing BAM channel creation when trimBam is on but PMD is off

Author: jfy133

main.nf

@@ -1643,47 +1643,42 @@ process bam_trim {
     """
 }
 
-
 if ( params.run_genotyping && params.genotyping_source == 'raw' ) {
     ch_rmdup_for_skipdamagemanipulation.mix(ch_output_from_pmdtools,ch_output_from_bamutils)
         .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes }
-
     ch_rmdupindex_for_skipdamagemanipulation.mix(ch_outputindex_from_pmdtools,ch_outputindex_from_bamutils)
         .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes }
-
 } else if ( params.run_genotyping && params.genotyping_source == "trimmed" )  {
     ch_rmdup_for_skipdamagemanipulation.mix(ch_output_from_pmdtools,ch_output_from_bamutils)
         .filter { it =~/.*trimmed.bam/ }
         .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes } 
-
     ch_rmdupindex_for_skipdamagemanipulation.mix(ch_outputindex_from_pmdtools,ch_outputindex_from_bamutils)
         .filter { it =~/.*trimmed.bam.bai|.*.trimmed.bam.csi/ }
         .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes }
-
 } else if ( params.run_genotyping && params.genotyping_source == "pmd" )  {
     ch_rmdup_for_skipdamagemanipulation.mix(ch_output_from_pmdtools,ch_output_from_bamutils)
         .filter { it =~/.*pmd.bam/ }
         .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes } 
-
     ch_rmdupindex_for_skipdamagemanipulation.mix(ch_outputindex_from_pmdtools,ch_outputindex_from_bamutils)
         .filter { it =~/.*pmd.bam.bai|.*.pmd.bam.csi/ }
         .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes }
-
 } else if ( !params.run_genotyping && !params.run_trim_bam && !params.run_pmdtools )  {
     ch_rmdup_for_skipdamagemanipulation
         .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes } 
-
     ch_rmdupindex_for_skipdamagemanipulation
-        .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes } 
+        .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes }
 } else if ( !params.run_genotyping && !params.run_trim_bam && params.run_pmdtools )  {
     ch_rmdup_for_skipdamagemanipulation
         .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes } 
-
     ch_rmdupindex_for_skipdamagemanipulation
-        .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes } 
+        .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes }
+} else if ( !params.run_genotyping && params.run_trim_bam && !params.run_pmdtools )  {
+    ch_rmdup_for_skipdamagemanipulation
+        .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes } 
+    ch_rmdupindex_for_skipdamagemanipulation
+        .into { ch_damagemanipulationindex_for_skipgenotyping; ch_damagemanipulationindex_for_genotyping_hc; ch_damagemanipulationindex_for_genotyping_freebayes }
 }
 
-
 /*
  Step 12a: Genotyping - UnifiedGenotyper Downloading
  NB: GATK 3.5 is the last release with VCF output in "old" VCF format, not breaking downstream tools. Therefore we need it (for now at least until downstream tools can read proper 4.2 VCFs... )