Added output files to ASCAT (#1820)

* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml

* added outputs + prefix to outputs

* added test-yml outputs

* change underscores to dots

modules/ascat/main.nf

@@ -17,12 +17,14 @@ process ASCAT {
     path(rt_file)   // optional
 
     output:
-    tuple val(meta), path("*png"),                             emit: png
+    tuple val(meta), path("*alleleFrequencies_chr*.txt"),      emit: allelefreqs
+    tuple val(meta), path("*BAF.txt"),                         emit: bafs
     tuple val(meta), path("*cnvs.txt"),                        emit: cnvs
+    tuple val(meta), path("*LogR.txt"),                        emit: logrs
     tuple val(meta), path("*metrics.txt"),                     emit: metrics
+    tuple val(meta), path("*png"),                             emit: png
     tuple val(meta), path("*purityploidy.txt"),                emit: purityploidy
     tuple val(meta), path("*segments.txt"),                    emit: segments
-    tuple val(meta), path("*alleleFrequencies_chr*.txt"),      emit: allelefreqs
     path "versions.yml",                                       emit: versions
 
     when:
@@ -64,8 +66,8 @@ process ASCAT {
     ascat.prepareHTS(
         tumourseqfile = "$input_tumor",
         normalseqfile = "$input_normal",
-        tumourname = "Tumour",
-        normalname = "Normal",
+        tumourname = paste0("$prefix", ".tumour"),
+        normalname = paste0("$prefix", ".normal"),
         allelecounter_exe = "alleleCounter",
         alleles.prefix = allele_prefix,
         loci.prefix = loci_prefix,
@@ -85,16 +87,16 @@ process ASCAT {
 
     #Load the data
     ascat.bc = ascat.loadData(
-        Tumor_LogR_file = "Tumour_tumourLogR.txt",
-        Tumor_BAF_file = "Tumour_normalBAF.txt",
-        Germline_LogR_file = "Tumour_normalLogR.txt",
-        Germline_BAF_file = "Tumour_normalBAF.txt",
+        Tumor_LogR_file = paste0("$prefix", ".tumour_tumourLogR.txt"),
+        Tumor_BAF_file = paste0("$prefix", ".tumour_tumourBAF.txt"),
+        Germline_LogR_file = paste0("$prefix", ".tumour_normalLogR.txt"),
+        Germline_BAF_file = paste0("$prefix", ".tumour_normalBAF.txt"),
         genomeVersion = "$genomeVersion",
         gender = "$gender"
     )
 
     #Plot the raw data
-    ascat.plotRawData(ascat.bc, img.prefix = "Before_correction_")
+    ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".before_correction."))
 
     # optional LogRCorrection
     if("$gc_input" != "NULL") {
@@ -104,12 +106,12 @@ process ASCAT {
             rt_input = paste0(normalizePath("$rt_input"), "/", "$rt_input", ".txt")
             ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = rt_input)
             #Plot raw data after correction
-            ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_")
+            ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc_rt."))
         }
         else {
             ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = $rt_input)
             #Plot raw data after correction
-            ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_RT_")
+            ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc."))
         }
     }
 
@@ -165,26 +167,27 @@ process ASCAT {
 
     """
 
-
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    echo stub > ${prefix}.after_correction.gc_rt.test.tumour.germline.png
+    echo stub > ${prefix}.after_correction.gc_rt.test.tumour.tumour.png
+    echo stub > ${prefix}.before_correction.test.tumour.germline.png
+    echo stub > ${prefix}.before_correction.test.tumour.tumour.png
     echo stub > ${prefix}.cnvs.txt
     echo stub > ${prefix}.metrics.txt
+    echo stub > ${prefix}.normal_alleleFrequencies_chr21.txt
+    echo stub > ${prefix}.normal_alleleFrequencies_chr22.txt
     echo stub > ${prefix}.purityploidy.txt
     echo stub > ${prefix}.segments.txt
-    echo stub > Tumour.ASCATprofile.png
-    echo stub > Tumour.ASPCF.png
-    echo stub > Before_correction_Tumour.germline.png
-    echo stub > After_correction_GC_Tumour.germline.png
-    echo stub > Tumour.rawprofile.png
-    echo stub > Tumour.sunrise.png
-    echo stub > Before_correction_Tumour.tumour.png
-    echo stub > After_correction_GC_Tumour.tumour.png
-    echo stub > Tumour_alleleFrequencies_chr21.txt
-    echo stub > Tumour_alleleFrequencies_chr22.txt
-    echo stub > Normal_alleleFrequencies_chr21.txt
-    echo stub > Normal_alleleFrequencies_chr22.txt
+    echo stub > ${prefix}.tumour.ASPCF.png
+    echo stub > ${prefix}.tumour.sunrise.png
+    echo stub > ${prefix}.tumour_alleleFrequencies_chr21.txt
+    echo stub > ${prefix}.tumour_alleleFrequencies_chr22.txt
+    echo stub > ${prefix}.tumour_normalBAF.txt
+    echo stub > ${prefix}.tumour_normalLogR.txt
+    echo stub > ${prefix}.tumour_tumourBAF.txt
+    echo stub > ${prefix}.tumour_tumourLogR.txt
 
     echo "${task.process}:" > versions.yml
     echo ' alleleCounter: 4.3.0' >> versions.yml

tests/modules/ascat/test.yml

@@ -3,17 +3,21 @@
   tags:
     - ascat
   files:
-    - path: output/ascat/After_correction_GC_Tumour.germline.png
-    - path: output/ascat/After_correction_GC_Tumour.tumour.png
-    - path: output/ascat/Before_correction_Tumour.germline.png
-    - path: output/ascat/Before_correction_Tumour.tumour.png
-    - path: output/ascat/Normal_alleleFrequencies_chr21.txt
-    - path: output/ascat/Normal_alleleFrequencies_chr22.txt
+    - path: output/ascat/test.after_correction.gc_rt.test.tumour.germline.png
+    - path: output/ascat/test.after_correction.gc_rt.test.tumour.tumour.png
+    - path: output/ascat/test.before_correction.test.tumour.germline.png
+    - path: output/ascat/test.before_correction.test.tumour.tumour.png
     - path: output/ascat/test.cnvs.txt
+    - path: output/ascat/test.metrics.txt
+    - path: output/ascat/test.normal_alleleFrequencies_chr21.txt
+    - path: output/ascat/test.normal_alleleFrequencies_chr22.txt
     - path: output/ascat/test.purityploidy.txt
     - path: output/ascat/test.segments.txt
-    - path: output/ascat/Tumour_alleleFrequencies_chr21.txt
-    - path: output/ascat/Tumour_alleleFrequencies_chr22.txt
-    - path: output/ascat/Tumour.ASCATprofile.png
-    - path: output/ascat/Tumour.rawprofile.png
-    - path: output/ascat/Tumour.sunrise.png
+    - path: output/ascat/test.tumour.ASPCF.png
+    - path: output/ascat/test.tumour.sunrise.png
+    - path: output/ascat/test.tumour_alleleFrequencies_chr21.txt
+    - path: output/ascat/test.tumour_alleleFrequencies_chr22.txt
+    - path: output/ascat/test.tumour_normalBAF.txt
+    - path: output/ascat/test.tumour_normalLogR.txt
+    - path: output/ascat/test.tumour_tumourBAF.txt
+    - path: output/ascat/test.tumour_tumourLogR.txt