Merge branch 'dev' into rename

Plant-Food-Research-Open · Aug 19, 2024 · cea7bae · cea7bae
2 parents 10fc01c + 89f53e8
commit cea7bae
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Showing 7 changed files with 27 additions and 29 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -44,6 +44,9 @@ jobs:
         with:
           version: "23.04.4"
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run stub-test
         run: |
           nextflow run \

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## 0.4.0+dev - [15-Aug-2024]
+## 0.4.0+dev - [19-Aug-2024]
 
 ### `Added`
 

diff --git a/conf/test.config b/conf/test.config
@@ -1,15 +1,7 @@
 params {
-    input               = 'tests/minimal/assemblysheet.csv'
-    protein_evidence    = 'https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/proteins.fa'
-}
+    input                   = "${projectDir}/tests/minimal/assemblysheet.csv"
+    protein_evidence        = 'https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/proteins.fa'
 
-// Additional args to BRAKER should be passed through braker_extra_args
-// The config below is only for test purposes
-process {
-    withName: '.*:FASTA_BRAKER3:BRAKER3' {
-        ext.args = [
-            '-gff3',
-            '--gm_max_intergenic 10000 --skipOptimize' // Not recommended! Used here to make the test execute faster
-        ].join(' ').trim()
-    }
+    braker_extra_args       = '--gm_max_intergenic 10000 --skipOptimize' // Added for faster test execution! Do not use with actual data!
+    busco_lineage_datasets  = 'eudicots_odb10'
 }
diff --git a/local_genepal b/local_genepal
@@ -18,5 +18,6 @@ nextflow run \
     -resume \
     $stub \
     --max_cpus 8 \
-    --max_memory '32.GB'
-    # --eggnogmapper_db_dir ../dbs/emapperdb/5.0.2
+    --max_memory '32.GB' \
+    --eggnogmapper_tax_scope 33090 \
+    --eggnogmapper_db_dir ../dbs/emapperdb/5.0.2
diff --git a/nextflow.config b/nextflow.config
@@ -57,19 +57,7 @@ params {
     validationS3PathCheck       = true
 }
 
-manifest {
-    name                        = 'genepal'
-    author                      = """Usman Rashid, Jason Shiller"""
-    homePage                    = 'https://github.com/PlantandFoodResearch/genepal'
-    description                 = """A NextFlow pipeline for pan-genome annotation"""
-    mainScript                  = 'main.nf'
-    nextflowVersion             = '!>=23.04.4'
-    version                     = '0.4.0+dev'
-    doi                         = ''
-}
-
 includeConfig './conf/base.config'
-includeConfig './conf/modules.config'
 
 profiles {
     apptainer {
@@ -104,3 +92,16 @@ trace {
     enabled                     = true
     file                        = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
+
+manifest {
+    name                        = 'pangene'
+    author                      = """Usman Rashid, Jason Shiller"""
+    homePage                    = 'https://github.com/PlantandFoodResearch/pangene'
+    description                 = """A NextFlow pipeline for pan-genome annotation"""
+    mainScript                  = 'main.nf'
+    nextflowVersion             = '!>=23.04.4'
+    version                     = '0.4.0+dev'
+    doi                         = ''
+}
+
+includeConfig './conf/modules.config'
diff --git a/tests/minimal/assemblysheet.csv b/tests/minimal/assemblysheet.csv
@@ -1,2 +1,2 @@
 tag,fasta,is_masked
-test,https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/genome.fa,yes
+a_thaliana,https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/genome.fa,yes
diff --git a/tests/minimal/params.json b/tests/minimal/params.json
@@ -1,5 +1,6 @@
 {
     "input": "tests/minimal/assemblysheet.csv",
     "protein_evidence": "https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/proteins.fa",
-    "braker_extra_args": "--gm_max_intergenic 10000 --skipOptimize"
+    "braker_extra_args": "--gm_max_intergenic 10000 --skipOptimize",
+    "busco_lineage_datasets": "eudicots_odb10"
 }