nf-test for pilon (#5293)

* nf-test for pilon * linting for license * Add stub and extra test * Swap to testdata_base_path * Add missing END_VERSIONS and alignment * Add optional outputs to stub --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
nf-core · Jun 27, 2024 · 0aef8ea · 0aef8ea
1 parent 5438150
commit 0aef8ea
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Showing 9 changed files with 481 additions and 41 deletions.
diff --git a/modules/nf-core/pilon/main.nf b/modules/nf-core/pilon/main.nf
@@ -9,7 +9,7 @@ process PILON {
 
     input:
     tuple val(meta), path(fasta)
-    tuple val(meta_bam), path(bam), path(bai)
+    tuple val(meta2), path(bam), path(bai)
     val pilon_mode
 
     output:
@@ -24,8 +24,8 @@ process PILON {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args       = task.ext.args ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}"
     def valid_mode = ["frags", "jumps", "unpaired", "bam"]
     if ( !valid_mode.contains(pilon_mode) )  { error "Unrecognised mode to run Pilon. Options: ${valid_mode.join(', ')}" }
     """
@@ -39,5 +39,24 @@ process PILON {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         pilon: \$(echo \$(pilon --version) | sed 's/^.*version //; s/ .*\$//' )
+    END_VERSIONS
     """
+
+    stub:
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def valid_mode = ["frags", "jumps", "unpaired", "bam"]
+    if ( !valid_mode.contains(pilon_mode) )  { error "Unrecognised mode to run Pilon. Options: ${valid_mode.join(', ')}" }
+    """
+    touch ${prefix}.fasta
+    touch ${prefix}.vcf
+    touch ${prefix}.change
+    touch ${prefix}.bed
+    touch ${prefix}.wig
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pilon: \$(echo \$(pilon --version) | sed 's/^.*version //; s/ .*\$//' )
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/pilon/meta.yml b/modules/nf-core/pilon/meta.yml
@@ -11,17 +11,22 @@ tools:
       documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage"
       tool_dev_url: "https://github.com/broadinstitute/pilon"
       doi: "10.1371/journal.pone.0112963"
-      licence: "['GPL v2']"
+      licence: ["GPL-2.0-or-later"]
 input:
   - meta:
       type: map
       description: |
-        Groovy Map containing sample information
+        Groovy Map containing sample information for the fasta
         e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: FASTA of the input genome
       pattern: "*.{fasta}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information for the bam file
+        e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
       description: BAM file of reads aligned to the input genome

diff --git a/modules/nf-core/pilon/tests/main.nf.test b/modules/nf-core/pilon/tests/main.nf.test
@@ -0,0 +1,116 @@
+nextflow_process {
+
+    name "Test Process PILON"
+    script "../main.nf"
+    process "PILON"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pilon"
+
+
+    test("homo sapiens bam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "bam"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens bam - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "bam"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens frags") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "frags"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens frags - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "frags"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}