QUILT nf-test and bamlist

modules/nf-core/quilt/quilt/environment.yml

@@ -4,4 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-quilt=1.0.5
+  - bioconda::r-quilt=1.0.5=r43h06b5641_0
+  - r-base=4.3.1

modules/nf-core/quilt/quilt/main.nf

@@ -8,7 +8,7 @@ process QUILT_QUILT {
         'biocontainers/r-quilt:1.0.5--r43h06b5641_0' }"
 
     input:
-    tuple val(meta), path(bams), path(bais), path(bamlist), path(reference_haplotype_file), path(reference_legend_file), val(chr), val(regions_start), val(regions_end), val(ngen), val(buffer), path(genetic_map_file)
+    tuple val(meta), path(bams), path(bais), path(reference_haplotype_file), path(reference_legend_file), val(chr), val(regions_start), val(regions_end), val(ngen), val(buffer), path(genetic_map_file)
     tuple val(meta2), path(posfile), path(phasefile)
     tuple val(meta3), path(fasta)
 
@@ -27,18 +27,18 @@ process QUILT_QUILT {
     def prefix                      =   task.ext.prefix ?: "${meta.id}"
     def extensions                  =   bams.collect { it.extension }
     def extension                   =   extensions.flatten().unique()
-    def list_command                =   extension == ["bam"]  ? "--bamlist=${bamlist}"                       :
-                                        extension == ["cram"] ? "--cramlist=${bamlist} --reference=${fasta}" : ""
+    def list_command                =   extension == ["bam"]  ? "--bamlist="                       :
+                                        extension == ["cram"] ? "--reference=${fasta} --cramlist=" : ""
     def genetic_map_file_command    =   genetic_map_file      ? "--genetic_map_file=${genetic_map_file}"     : ""
     def posfile_command             =   posfile               ? "--posfile=${posfile}"                       : ""
     def phasefile_command           =   phasefile             ? "--phasefile=${phasefile}"                   : ""
     if (!(args ==~ /.*--seed.*/)) {args += " --seed=1"}
 
     """
-
+    printf "%s\\n" $bams | tr -d '[],' > all_files.txt
 
     QUILT.R \\
-        $list_command \\
+        ${list_command}all_files.txt \\
         $genetic_map_file_command \\
         $posfile_command \\
         $phasefile_command \\

modules/nf-core/quilt/quilt/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/rwdavies/quilt"
       tool_dev_url: "https://github.com/rwdavies/quilt"
       doi: "10.1038/s41588-021-00877-0"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -28,10 +28,6 @@ input:
       type: file
       description: (Mandatory) BAM/CRAM index files
       pattern: "*.{bai}"
-  - bamlist:
-      type: file
-      description: (Mandatory) "Path to file with bam file locations. File is one row per entry, path to bam files. Bam index files should exist in same directory as for each bam, suffixed either .bam.bai or .bai.
-      pattern: "*.{txt}"
   - reference_haplotype_file:
       type: file
       description: (Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1)
@@ -99,9 +95,12 @@ output:
       type: file
       description: TBI file of the VCF.
       pattern: "*.{vcf.gz.tbi}"
-  - RData:
+  - rdata:
       type: directory
       description: Optional directory path to prepared RData file with reference objects (useful with --save_prepared_reference=TRUE).
+  - plots:
+      type: directory
+      description: Optional directory path to save plots.
 authors:
   - "@atrigila"
 maintainers:

modules/nf-core/quilt/quilt/tests/main.nf.test

@@ -0,0 +1,132 @@
+// Input data
+def path = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/"
+def bam  = "[${path}NA12878.haplotagged.1.0.bam', checkIfExists: true), ${path}NA12878.ont.1.0.bam', checkIfExists: true), ${path}NA12878.illumina.1.0.bam', checkIfExists: true)]"
+def bai  = "[${path}NA12878.haplotagged.1.0.bam.bai', checkIfExists: true), ${path}NA12878.ont.1.0.bam.bai', checkIfExists: true),${path}NA12878.illumina.1.0.bam.bai', checkIfExists: true)]"
+
+// Input reference data
+def reference_haplotype_file = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.hap.gz', checkIfExists: true)"
+def reference_legend_file    = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.noNA12878.legend.gz', checkIfExists: true)"
+def genetic_map_file         = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/CEU-chr20-final.b38.txt.gz', checkIfExists: true)"
+
+// Parameters
+def chr           = "'chr20'"
+def regions_start = "2000001"
+def regions_end   = "2100000"
+def ngen          = "100"
+def buffer        = "10000"
+
+
+// (optional) input truth data
+def posfile   = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.posfile.txt', checkIfExists: true)"
+def phasefile = "file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/quilt/ALL.chr20_GRCh38.genotypes.20170504.chr20.2000001.2100000.phasefile.txt', checkIfExists: true)"
+def posfile_phasefile = "[[ id:'test', chr:'chr20' ], [$posfile], [$phasefile]]"
+def fasta = "[[id:'test'], []]"
+
+// Input channel quilt
+def ch_input = "[ id:'test', chr:'chr20' ], $bam, $bai, [$reference_haplotype_file], [$reference_legend_file], $chr, $regions_start, $regions_end, $ngen, $buffer"
+def ch_input_gmap = "[$ch_input, [$genetic_map_file]]"
+def ch_input_nogmap = "[$ch_input, []]"
+
+nextflow_process {
+
+    name "Test Process QUILT"
+    script "../main.nf"
+    process "QUILT_QUILT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "quilt/quilt"
+    tag "quilt"
+
+    test("QUILT") {
+        config ("./quilt_default.config")
+        when {
+            process {
+                """
+                input[0] = $ch_input_gmap
+                input[1] = $posfile_phasefile
+                input[2] = $fasta
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("QUILT no optional files") {
+        config ("./quilt_default.config")
+        when {
+            process {
+                """
+                input[0] = $ch_input_nogmap
+                input[1] = [[id: null], [], []]
+                input[2] = $fasta
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("QUILT optional output") {
+        config ("./quilt_optional.config")
+        when {
+            process {
+                """
+                input[0] = $ch_input_gmap
+                input[1] = $posfile_phasefile
+                input[2] = $fasta
+                """
+            }
+        }
+
+        then {
+            def dir = new File(process.out.plots[0][1])
+            def list = []
+            dir.eachFileRecurse { file -> list << file.getName() }
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf + process.out.tbi +
+                    list.sort() +
+                    process.out.rdata + process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("QUILT no seed") {
+        config ("./quilt_noseed.config")
+        when {
+            process {
+                """
+                input[0] = $ch_input_gmap
+                input[1] = $posfile_phasefile
+                input[2] = $fasta
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}