From fa28176af60ff15e1bb0edf9e8a5a4b77113ec36 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Mon, 16 Dec 2024 13:28:31 +1300
Subject: [PATCH] Fixed post-liftoff merge

---
 CHANGELOG.md                             |  1 +
 subworkflows/local/fasta_liftoff/main.nf | 21 ++++++++++++++++++++-
 tests/stub/main.nf.test.snap             | 22 ++--------------------
 3 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9937888..a274d90 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 2. Switched branch name from `master` to `main` in the GHA CIs
 3. Fixed an issue in `genepal_report.Rmd` which caused the pangene matrix plot to fail when the number of clusters exceeded 65536 [#124](https://github.com/Plant-Food-Research-Open/genepal/issues/124)
 4. Fixed an issue where `GENEPALREPORT` process failed due to OOM kill signal from SLURM [#123](https://github.com/Plant-Food-Research-Open/genepal/issues/123)
+5. Fixed an issue where Gff merge after liftoff failed when one of the Gff files did not contain any genes
 
 ### `Dependencies`
 
diff --git a/subworkflows/local/fasta_liftoff/main.nf b/subworkflows/local/fasta_liftoff/main.nf
index d1d818f..559c0b2 100644
--- a/subworkflows/local/fasta_liftoff/main.nf
+++ b/subworkflows/local/fasta_liftoff/main.nf
@@ -88,7 +88,26 @@ workflow FASTA_LIFTOFF {
     )
 
     ch_liftoff_gff3                 = LIFTOFF.out.polished_gff3
-                                    | map { meta, gff -> [ [ id: meta.target_assembly ], gff ] }
+                                    | map { meta, gff ->
+
+                                        def gene_count = gff.readLines()
+                                            .findAll { it ->
+                                                if ( it.startsWith('#') ) { return false }
+
+                                                def cols = it.split('\t')
+                                                def feat = cols[2]
+
+                                                if ( feat != 'gene' ) { return false }
+
+                                                return true
+                                            }.size()
+
+                                        // To avoid failure in AGAT_SPMERGEANNOTATIONS
+                                        // when one of the GFF files is empty
+                                        if ( gene_count < 1 ) { return null }
+
+                                        [ [ id: meta.target_assembly ], gff ]
+                                    }
                                     | groupTuple
 
     ch_versions                     = ch_versions.mix(LIFTOFF.out.versions.first())
diff --git a/tests/stub/main.nf.test.snap b/tests/stub/main.nf.test.snap
index 7ed6f6e..d96bf68 100644
--- a/tests/stub/main.nf.test.snap
+++ b/tests/stub/main.nf.test.snap
@@ -2,7 +2,7 @@
     "full - stub": {
         "content": [
             {
-                "successful tasks": 166,
+                "successful tasks": 126,
                 "versions": {
                     "AGAT_CONVERTSPGFF2GTF": {
                         "agat": "v1.4.0"
@@ -16,15 +16,6 @@
                     "AGAT_SPEXTRACTSEQUENCES": {
                         "agat": "v1.4.0"
                     },
-                    "AGAT_SPFILTERFEATUREFROMKILLLIST": {
-                        "agat": "v1.4.0"
-                    },
-                    "AGAT_SPFLAGSHORTINTRONS": {
-                        "agat": "v1.4.1"
-                    },
-                    "AGAT_SPMERGEANNOTATIONS": {
-                        "agat": "v1.4.0"
-                    },
                     "BENCHMARK": {
                         "gffcompare": "0.12.6"
                     },
@@ -46,9 +37,6 @@
                     "CAT_PROTEIN_FASTAS": {
                         "pigz": "2.3.4"
                     },
-                    "COMPARE_BRAKER_TO_LIFTOFF": {
-                        "gffcompare": "0.12.6"
-                    },
                     "CUSTOM_SRATOOLSNCBISETTINGS": {
                         "sratools": "3.0.8"
                     },
@@ -79,9 +67,6 @@
                     "GFF2FASTA_FOR_EGGNOGMAPPER": {
                         "gffread": "0.12.7"
                     },
-                    "GFFREAD_AFTER_LIFTOFF": {
-                        "gffread": "0.12.7"
-                    },
                     "GFFREAD_BEFORE_LIFTOFF": {
                         "gffread": "0.12.7"
                     },
@@ -106,9 +91,6 @@
                     "LIFTOFF": {
                         "liftoff": "v1.6.3"
                     },
-                    "MERGE_LIFTOFF_ANNOTATIONS": {
-                        "agat": "v1.4.0"
-                    },
                     "ORTHOFINDER": {
                         "orthofinder": "2.5.5"
                     },
@@ -208,6 +190,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-12-11T21:51:12.841395"
+        "timestamp": "2024-12-16T13:24:49.69503"
     }
 }
\ No newline at end of file