Merge pull request #909 from nf-core/pileupcaller_paths_fix

Pileupcaller paths fix

Author: jfy133

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#895](https://github.com/nf-core/eager/issues/895) Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting)
 - [#897](https://github.com/nf-core/eager/issues/897) Fix pipeline crash if no Kraken2 results generated (♥ to @alexandregilardet for reporting)
 - [#899](https://github.com/nf-core/eager/issues/897) Fix pipeline crash for circulargenerator if reference file does not end in .fasta (♥ to @scarlhoff for reporting)
+- Fix staging of input bams for genotyping_pileupcaller process. Downstream changes from changes introduced when fixing endorspy caching.
 
 ### `Dependencies`
 

main.nf

@@ -1787,7 +1787,7 @@ if (params.run_bam_filtering) {
         def seqtype = it[3]
         def organism = it[4]
         def strandedness = it[5]
-        def udg = it[6]     
+        def udg = it[6]
         def stats = file(it[7])
         def poststats = file("$projectDir/assets/nf-core_eager_dummy.txt")
 
@@ -2229,7 +2229,7 @@ process bam_trim {
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_bamutils_decision.totrim
 
     output: 
-    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.trimmed.bam"), file("*.trimmed.bam.{bai,csi}") into ch_trimmed_from_bamutils
+    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.trimmed.bam"), path("*.trimmed.bam.{bai,csi}") into ch_trimmed_from_bamutils
 
     script:
     def softclip = params.bamutils_softclip ? '-c' : '' 
@@ -2261,7 +2261,7 @@ ch_trimmed_formerge = ch_bamutils_decision.notrim
         def seqtype = it[3]
         def organism = it[4]
         def strandedness = it[5]
-        def udg = it[6]     
+        def udg = it[6]
         def bam = it[7].flatten()
         def bai = it[8].flatten()
 
@@ -2487,10 +2487,36 @@ ch_damagemanipulation_for_genotyping_pileupcaller
  // Create pileupcaller input tuples
 ch_input_for_genotyping_pileupcaller.singleStranded
   .groupTuple(by:[5])
+  .map{
+        def samplename = it[0]
+        def libraryid  = it[1]
+        def lane = it[2]
+        def seqtype = it[3]
+        def organism = it[4]
+        def strandedness = it[5]
+        def udg = it[6]
+        def bam = it[7].flatten()
+        def bai = it[8].flatten()
+
+      [samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai ]
+  }
   .set {ch_prepped_for_pileupcaller_single}
 
 ch_input_for_genotyping_pileupcaller.doubleStranded
   .groupTuple(by:[5])
+  .map{
+        def samplename = it[0]
+        def libraryid  = it[1]
+        def lane = it[2]
+        def seqtype = it[3]
+        def organism = it[4]
+        def strandedness = it[5]
+        def udg = it[6]
+        def bam = it[7].flatten()
+        def bai = it[8].flatten()
+
+      [samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai ]
+  }
   .set {ch_prepped_for_pileupcaller_double}
 
 process genotyping_pileupcaller {
@@ -2502,7 +2528,7 @@ process genotyping_pileupcaller {
   params.run_genotyping && params.genotyping_tool == 'pileupcaller'
 
   input:
-  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai from ch_prepped_for_pileupcaller_double.mix(ch_prepped_for_pileupcaller_single)
+  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_prepped_for_pileupcaller_double.mix(ch_prepped_for_pileupcaller_single)
   file fasta from ch_fasta_for_genotyping_pileupcaller.collect()
   file fai from ch_fai_for_pileupcaller.collect()
   file dict from ch_dict_for_pileupcaller.collect()