Get tests for all of proteinannotator to run

Author: olgabot

subworkflows/local/functional_annotation/main.nf

@@ -13,15 +13,14 @@ workflow FUNCTIONAL_ANNOTATION {
 
     // Create a multifasta, with one fasta per entry, add the sequence ID to the meta id
     ch_fasta
-        .splitFasta(file: true)
-        .view()
         .map {
             meta, fasta ->
-                [
-                    [id: "${meta.id}_${fasta.splitFasta(record: [id: true]).id[0].replaceAll(/\|/, '-')}"],
-                    fasta
-                ]
+            [
+                [id:"${meta.id}_${fasta[0].splitFasta(record: [id: true]).id[0].replaceAll(/\|/, '-')}"] ,
+                fasta[0].splitFasta(file:true)
+            ]
         }
+        .transpose()
         .view()
         .set { ch_multifasta }
 

tests/.nftignore

@@ -1,4 +1,9 @@
 .DS_Store
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_general_stats.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/multiqc_sources.txt
 pipeline_info/*.{html,json,txt,yml}

tests/default.nf.test.snap

@@ -26,11 +26,7 @@
                 "seqkit/T1026.tsv"
             ],
             [
-                "multiqc.log:md5,f9afd4d93d7620d65ce5d6360339ff6e",
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
-                "multiqc_data.json:md5,eba015690f3d2ddf54967a237db11b0e",
-                "multiqc_software_versions.txt:md5,c5b754560c24cc8da0c1e92febf6f37f",
-                "multiqc_sources.txt:md5,d2a044df39ce3c6abe5cdc2d67473490",
                 "T1024.tsv:md5,c8a3fd71b27b9455aa837e1d50026971",
                 "T1026.tsv:md5,b028126e117cf0979b6f907cb20c6958"
             ]
@@ -39,6 +35,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.1"
         },
-        "timestamp": "2025-05-14T11:49:14.001221"
+        "timestamp": "2025-05-14T16:07:27.013727"
     }
-}
+}

workflows/proteinannotator.nf

@@ -26,6 +26,8 @@ workflow PROTEINANNOTATOR {
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
+    ch_samplesheet.view()
+
     FUNCTIONAL_ANNOTATION (
         ch_samplesheet
     )