Orthofinder

modules/nf-core/orthofinder/main.nf

@@ -9,6 +9,7 @@ process ORTHOFINDER {
 
     input:
     tuple val(meta), path(fastas, stageAs: 'input/')
+    path(prior_run)
 
     output:
     tuple val(meta), path("$prefix")    , emit: orthofinder
@@ -18,22 +19,28 @@ process ORTHOFINDER {
     task.ext.when == null || task.ext.when
 
     script:
-    def args    = task.ext.args ?: ''
-    prefix      = task.ext.prefix ?: "${meta.id}"
+    def args   = task.ext.args   ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def include_command = prior_run   ? "-b $prior_run" : ''
+
     """
     mkdir temp_pickle
 
     orthofinder \\
-        $args \\
         -t $task.cpus \\
         -a $task.cpus \\
         -p temp_pickle \\
         -f input \\
-        -n $prefix
+        -n $prefix \\
+        $include_command $args
+
+    if [ -e input/OrthoFinder/Results_$prefix ]; then
+        mv input/OrthoFinder/Results_$prefix $prefix
+    fi
 
-    mv \\
-        input/OrthoFinder/Results_$prefix \\
-        $prefix
+    if [ -e WorkingDirectory/OrthoFinder/Results_$prefix ]; then
+        mv WorkingDirectory/OrthoFinder/Results_$prefix $prefix
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -42,8 +49,10 @@ process ORTHOFINDER {
     """
 
     stub:
-    def args    = task.ext.args ?: ''
-    prefix      = task.ext.prefix ?: "${meta.id}"
+    def args   = task.ext.args   ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def include_command = prior_run   ? "-b $prior_run" : ''
+
     """
     mkdir -p    $prefix/Comparative_Genomics_Statistics
     mkdir       $prefix/Gene_Duplication_Events

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

@@ -28,6 +28,7 @@ nextflow_process {
                     [ id:'test', single_end:false ],
                     [ file_a, file_b ]
                 ]
+                input[1] = []
                 """
             }
         }
@@ -41,8 +42,6 @@ nextflow_process {
                 all_files << file
             }
 
-            def all_file_names = all_files.collect { it.name }.sort(false)
-
             def stable_file_names = [
                 'Statistics_PerSpecies.tsv',
                 'SpeciesTree_Gene_Duplications_0.5_Support.txt',
@@ -52,7 +51,51 @@ nextflow_process {
             def stable_files = all_files.findAll { it.name in stable_file_names }
 
             assert snapshot(
-                all_file_names,
+                stable_files,
+                process.out.versions[0]
+            ).match()
+        }
+
+    }
+
+
+    test("sarscov2 - candidatus_portiera_aleyrodidarum - proteome - resume") {
+
+        when {
+            process {
+                """
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
+                    .copyTo("${workDir}/sarscov2.fasta")
+
+                def file_a = file("https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/sequences/H1065.fasta")
+                def file_c = file("s3://temporary-nfcore-module-data/test/WorkingDirectory")
+                input[0] = [
+                    [ id:'test_2', single_end:false ],
+                    [ file_a ]
+                ]
+                input[1] = file_c
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            def all_files = []
+
+            file(process.out.orthofinder[0][1]).eachFileRecurse (FileType.FILES) { file ->
+                all_files << file
+            }
+
+            def stable_file_names = [
+                'Statistics_PerSpecies.tsv',
+                'OrthologuesStats_Totals.tsv',
+                'Duplications_per_Species_Tree_Node.tsv'
+            ]
+
+            def stable_files = all_files.findAll { it.name in stable_file_names }
+
+            assert snapshot(
                 stable_files,
                 process.out.versions[0]
             ).match()
@@ -80,6 +123,7 @@ nextflow_process {
                     [ id:'test', single_end:false ],
                     [ file_a, file_b ]
                 ]
+                input[1] = []
                 """
             }
         }