Updated fasta_ltrretriever_lai to fix [ meta, [] ] bug

Plant-Food-Research-Open · May 2, 2024 · 0cc8a8a · 0cc8a8a
1 parent 5660e89
commit 0cc8a8a
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Showing 3 changed files with 78 additions and 43 deletions.
diff --git a/modules.json b/modules.json
@@ -81,7 +81,7 @@
                 "pfr": {
                     "fasta_ltrretriever_lai": {
                         "branch": "main",
-                        "git_sha": "10b046eaac396f279c08e7e2bb067482ccd9c74e",
+                        "git_sha": "8088445a270d324cb06e085f18790839c9684754",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_bwa_mem_samblaster": {

diff --git a/subworkflows/pfr/fasta_ltrretriever_lai/main.nf b/subworkflows/pfr/fasta_ltrretriever_lai/main.nf
@@ -32,6 +32,7 @@ workflow FASTA_LTRRETRIEVER_LAI {
                                     | join(
                                         ch_monoploid_seqs ?: Channel.empty()
                                     )
+                                    | filter { meta, tsv, seqs -> seqs } // Cater to channel: [ meta, tsv, [] ]
                                     | map { meta, short_ids_tsv, monoploid_seqs ->
                                         map_monoploid_seqs_to_new_ids(meta, short_ids_tsv, monoploid_seqs)
                                     }

diff --git a/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test b/subworkflows/pfr/fasta_ltrretriever_lai/tests/main.nf.test
@@ -18,22 +18,22 @@ nextflow_workflow {
     tag "ltrretriever/lai"
     tag "custom/restoregffids"
 
-    test("actinidia_chinensis-genome_21_fasta_gz") {
-
-        setup {
-            run("GUNZIP") {
-                script "../../../../modules/nf-core/gunzip"
-
-                process {
-                    """
-                    input[0] = [
-                        [ id:'test' ],
-                        file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
-                    ]
-                    """
-                }
+    setup {
+        run("GUNZIP") {
+            script "../../../../modules/nf-core/gunzip"
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['actinidia_chinensis']['genome']['genome_1_fasta_gz'], checkIfExists: true)
+                ]
+                """
             }
         }
+    }
+
+    test("actinidia_chinensis-genome_1_fasta_gz") {
 
         when {
             workflow {
@@ -57,23 +57,43 @@ nextflow_workflow {
         }
     }
 
-    test("actinidia_chinensis-genome_21_fasta_gz-with_mono") {
+    test("actinidia_chinensis-genome_1_fasta_gz-with_mono") {
 
-        setup {
-            run("GUNZIP") {
-                script "../../../../modules/nf-core/gunzip"
+        when {
+            workflow {
+                """
+                GUNZIP.out.gunzip.map { meta, fasta ->
+                    def fa          = new File('test.fa')
+                    fa.write(fasta.text.replaceAll('>chr1', '>chr_xxxxxxxxxxxxxxx_1'))
 
-                process {
-                    """
-                    input[0] = [
-                        [ id:'test' ],
-                        file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
-                    ]
-                    """
+                    [ meta, fa.toPath() ]
                 }
+                | set { ch_fa }
+
+                def monoploid_seqs  = new File('test.mono.seq.txt')
+                monoploid_seqs.write("chr_xxxxxxxxxxxxxxx_1")
+
+                input[0]            = ch_fa
+                input[1]            = Channel.of( [ [ id:'test' ], monoploid_seqs.toPath() ] )
+                input[2]            = false
+                """
             }
         }
 
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert file(workflow.out.annotation_gff[0][1]).text.contains('Copia_LTR_retrotransposon') },
+                { assert file(workflow.out.lai_log[0][1]).text.contains('Calculate LAI:') },
+                { assert file(workflow.out.lai_log[0][1]).text.contains('Done!') },
+                { assert Math.abs(Float.parseFloat(path(workflow.out.lai_out[0][1]).text.split("\n")[1].split("\t")[6]) - 31.29) <= 1.0 },
+                { assert file(workflow.out.ltrlib[0][1]).text.contains('#LTR/Copia') }
+            )
+        }
+    }
+
+    test("actinidia_chinensis-genome_1_fasta_gz-with_empty_mono_channel") {
+
         when {
             workflow {
                 """
@@ -85,11 +105,8 @@ nextflow_workflow {
                 }
                 | set { ch_fa }
 
-                def monoploid_seqs  = new File('test.mono.seq.txt')
-                monoploid_seqs.write("chr_xxxxxxxxxxxxxxx_1")
-
                 input[0]            = ch_fa
-                input[1]            = Channel.of( [ [ id:'test' ], monoploid_seqs.toPath() ] )
+                input[1]            = ch_fa.map { meta, fasta -> [ meta, [] ] }
                 input[2]            = false
                 """
             }
@@ -107,25 +124,42 @@ nextflow_workflow {
         }
     }
 
-    test("actinidia_chinensis-genome_21_fasta_gz-without_lai") {
+    test("actinidia_chinensis-genome_1_fasta_gz-with_empty_mono") {
 
-        options '-stub'
+        when {
+            workflow {
+                """
+                GUNZIP.out.gunzip.map { meta, fasta ->
+                    def fa          = new File('test.fa')
+                    fa.write(fasta.text.replaceAll('>chr1', '>chr_xxxxxxxxxxxxxxx_1'))
 
-        setup {
-            run("GUNZIP") {
-                script "../../../../modules/nf-core/gunzip"
-
-                process {
-                    """
-                    input[0] = [
-                        [ id:'test' ],
-                        file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
-                    ]
-                    """
+                    [ meta, fa.toPath() ]
                 }
+                | set { ch_fa }
+
+                input[0]            = ch_fa
+                input[1]            = []
+                input[2]            = false
+                """
             }
         }
 
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert file(workflow.out.annotation_gff[0][1]).text.contains('Copia_LTR_retrotransposon') },
+                { assert file(workflow.out.lai_log[0][1]).text.contains('Calculate LAI:') },
+                { assert file(workflow.out.lai_log[0][1]).text.contains('Done!') },
+                { assert Math.abs(Float.parseFloat(path(workflow.out.lai_out[0][1]).text.split("\n")[1].split("\t")[6]) - 31.29) <= 1.0 },
+                { assert file(workflow.out.ltrlib[0][1]).text.contains('#LTR/Copia') }
+            )
+        }
+    }
+
+    test("actinidia_chinensis-genome_1_fasta_gz-without_lai") {
+
+        options '-stub'
+
         when {
             workflow {
                 """