Fixed an issue where TSEBRA failed due to '.' in phase column from LIFTOFF

.github/workflows/branch.yml

@@ -1,15 +1,15 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to main branch on the repository
+# It fails when someone tries to make a PR against the Plant-Food-Research-Open `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches: [main]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'Plant-Food-Research-Open/genepal'
         run: |
@@ -22,7 +22,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +32,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch.
+            The `main` branch should always contain code from the latest release.
+            Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.github/workflows/download_pipeline.yml

@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,10 +17,10 @@ on:
       - edited
       - synchronize
     branches:
-      - master
+      - main
   pull_request_target:
     branches:
-      - master
+      - main
 
 env:
   NXF_ANSI_LOG: false

.nf-core.yml

@@ -30,5 +30,5 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 0.5.0
+  version: 0.5.1
 update: null

CHANGELOG.md

@@ -3,6 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.5.1 - [02-Dec-2024]
+
+### `Added`
+
+### `Fixed`
+
+1. Fixed an issue where TSEBRA failed because LIFTOFF mislabelled the phase of CDS features [#115](https://github.com/Plant-Food-Research-Open/genepal/issues/115)
+2. Switched branch name from `master` to `main` in the GHA CIs
+
+### `Dependencies`
+
+1. Nextflow!>=24.04.2
+2. [email protected]
+
+### `Deprecated`
+
 ## v0.5.0 - [21-Nov-2024]
 
 ### `Added`

CITATION.cff

@@ -31,7 +31,7 @@ authors:
   - family-names: "Thomson"
     given-names: "Susan"
 title: "genepal: A Nextflow pipeline for genome and pan-genome annotation"
-version: 0.5.0
+version: 0.5.1
 date-released: 2024-11-21
 url: "https://github.com/Plant-Food-Research-Open/genepal"
 doi: 10.5281/zenodo.14195006

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/plant-food-research-open/genepal" target="_blank">plant-food-research-open/genepal</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://github.com/plant-food-research-open/genepal/blob/0.5.0/docs/usage.md" target="_blank">documentation</a>.
+  <a href="https://github.com/plant-food-research-open/genepal/blob/0.5.1/docs/usage.md" target="_blank">documentation</a>.
 
 report_section_order:
   "plant-food-research-open-genepal-methods-description":

conf/modules.config

@@ -215,6 +215,11 @@ process { // SUBWORKFLOW: FASTA_LIFTOFF
         ext.args = '--keep-genes'
     }
 
+    withName: '.*:FASTA_LIFTOFF:GT_GFF3_AFTER_LIFTOFF' {
+        ext.prefix = { "${meta.id}.liftoff.fixed" }
+        ext.args = '-tidy -retainids -sort -addids no'
+    }
+
     withName: '.*:FASTA_LIFTOFF:GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST:AGAT_CONVERTSPGFF2GTF' {
         ext.args = '--gtf_version relax'
     }

nextflow.config

@@ -261,7 +261,7 @@ manifest {
     description     = """A Nextflow pipeline for consensus, phased and pan-genome annotation."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '0.5.0'
+    version         = '0.5.1'
     doi             = 'https://doi.org/10.5281/zenodo.14195006'
 }
 

subworkflows/local/fasta_liftoff.nf

@@ -6,6 +6,7 @@ include { AGAT_SPMERGEANNOTATIONS as MERGE_LIFTOFF_ANNOTATIONS  } from '../../mo
 include { AGAT_SPFLAGSHORTINTRONS                               } from '../../modules/gallvp/agat/spflagshortintrons/main'
 include { AGAT_SPFILTERFEATUREFROMKILLLIST                      } from '../../modules/nf-core/agat/spfilterfeaturefromkilllist/main'
 include { GFFREAD as GFFREAD_AFTER_LIFTOFF                      } from '../../modules/nf-core/gffread/main'
+include { GT_GFF3 as GT_GFF3_AFTER_LIFTOFF                      } from '../../modules/nf-core/gt/gff3/main'
 include { GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST                } from '../../subworkflows/local/gff_tsebra_spfilterfeaturefromkilllist'
 
 workflow FASTA_LIFTOFF {
@@ -120,8 +121,8 @@ workflow FASTA_LIFTOFF {
     ch_versions                     = ch_versions.mix(AGAT_SPFLAGSHORTINTRONS.out.versions.first())
 
     // COLLECTFILE: Kill list for valid_ORF=False transcripts
-    // tRNA, rRNA
-    // gene with any intron marked as 'pseudo=' by AGAT/SPFLAGSHORTINTRONS
+    // tRNA, rRNA, gene with any intron marked as
+    // 'pseudo=' by AGAT/SPFLAGSHORTINTRONS
     ch_kill_list                    = ch_flagged_gff
                                     | map { meta, gff ->
 
@@ -171,9 +172,16 @@ workflow FASTA_LIFTOFF {
     // MODULE: GFFREAD as GFFREAD_AFTER_LIFTOFF
     GFFREAD_AFTER_LIFTOFF ( ch_liftoff_purged_gff, [] )
 
-    ch_attr_trimmed_gff             = GFFREAD_AFTER_LIFTOFF.out.gffread_gff
     ch_versions                     = ch_versions.mix(GFFREAD_AFTER_LIFTOFF.out.versions.first())
 
+    // MODULE: GT_GFF3 as GT_GFF3_AFTER_LIFTOFF
+    // To fix the phase mislabelled by LIFTOFF
+    // https://github.com/Plant-Food-Research-Open/genepal/issues/115
+    GT_GFF3_AFTER_LIFTOFF ( GFFREAD_AFTER_LIFTOFF.out.gffread_gff )
+
+    ch_attr_trimmed_gff             = GT_GFF3_AFTER_LIFTOFF.out.gt_gff3
+    ch_versions                     = ch_versions.mix(GT_GFF3_AFTER_LIFTOFF.out.versions.first())
+
     // SUBWORKFLOW: GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST
     GFF_TSEBRA_SPFILTERFEATUREFROMKILLLIST(
         val_filter_liftoff_by_hints ? ch_attr_trimmed_gff : Channel.empty(),

tests/minimal/main.nf.test.snap

@@ -55,7 +55,7 @@
                         "tsebra": "1.1.2.5"
                     },
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v0.5.0"
+                        "plant-food-research-open/genepal": "v0.5.1"
                     }
                 },
                 "stable paths": [
@@ -82,8 +82,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T11:35:02.477202"
+        "timestamp": "2024-12-02T16:52:30.400922"
     }
-}
+}

tests/short/main.nf.test.snap

@@ -5,18 +5,18 @@
                 "successful tasks": 0,
                 "versions": {
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v0.5.0"
+                        "plant-food-research-open/genepal": "v0.5.1"
                     }
                 },
                 "stable paths": [
-
+                    
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-22T11:39:43.110621"
+        "timestamp": "2024-12-02T16:52:41.687179"
     }
-}
+}

tests/stub/main.nf.test.snap

@@ -2,7 +2,7 @@
     "full - stub": {
         "content": [
             {
-                "successful tasks": 154,
+                "successful tasks": 158,
                 "versions": {
                     "AGAT_CONVERTSPGFF2GTF": {
                         "agat": "v1.4.0"
@@ -79,6 +79,9 @@
                     "GT_GFF3": {
                         "genometools": "1.6.5"
                     },
+                    "GT_GFF3_AFTER_LIFTOFF": {
+                        "genometools": "1.6.5"
+                    },
                     "GUNZIP": {
                         "gunzip": 1.1
                     },
@@ -143,7 +146,7 @@
                         "tsebra": "1.1.2.5"
                     },
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v0.5.0"
+                        "plant-food-research-open/genepal": "v0.5.1"
                     }
                 },
                 "stable paths": [
@@ -191,6 +194,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-21T12:34:14.056074"
+        "timestamp": "2024-12-02T17:01:15.438026"
     }
-}
+}