Plant-Food-Research-Open · GallVp · Aug 19, 2024 · Aug 15, 2024 · Aug 15, 2024 · Aug 15, 2024
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,11 +1,11 @@
 # Adopted from https://github.com/nf-core/modules/blob/master/.github/workflows/test.yml
 
-name: Lint and -stub on Linux/Docker
+name: CI tests
 on:
   push:
-    branches: [main]
+    branches:
+      - dev
   pull_request:
-    branches: [main]
 
 # Cancel if a newer run is started
 concurrency:
@@ -30,7 +30,7 @@ jobs:
       - name: Run pre-commit
         run: pre-commit run --all-files
 
-  stub-test:
+  test:
     runs-on: ubuntu-latest
     name: Run stub test with docker
     env:
@@ -44,17 +44,20 @@ 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 \
             main.nf \
-            -profile local,docker \
+            -profile docker \
             -stub \
             -params-file tests/stub/params.json
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [pre-commit, stub-test]
+    needs: [pre-commit, test]
     if: always()
     steps:
       - name: All tests ok

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 - [07-Aug-2024]
+## 0.4.0+dev - [19-Aug-2024]
 
 ### `Added`
 
@@ -24,6 +24,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 15. Reduced `BRAKER3` threads to 8 [#55](https://github.com/PlantandFoodResearch/pangene/issues/55)
 16. Now the final annotations are stored in the `annotations` folder [#53](https://github.com/PlantandFoodResearch/pangene/issues/53)
 17. Added `-gff` flag to `REPEATMASKER` to save the gff file [#54](https://github.com/PlantandFoodResearch/pangene/issues/54)
+18. Now a single `fasta` file can be directly specified for `protein_evidence`
+19. `eggnogmapper_db_dir` is not a required parameter anymore
+20. `eggnogmapper_tax_scope` is now set to 1 (root div) by default
+21. Added a `test` profile based on public data
 
 ### `Fixed`
 
@@ -46,7 +50,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 6. Removed dependency on <https://github.com/kherronism/nf-modules.git> for `BRAKER3` and `REPEATMASKER` modules which are now installed from <https://github.com/GallVp/nxf-components.git>
 7. Removed dependency on <https://github.com/PlantandFoodResearch/nxf-modules.git>
 8. Now the final annotations are not stored in the `final` folder
-9. Now BRAKER3 outputs are not saved by default [#53](https://github.com/PlantandFoodResearch/pangene/issues/53)
+9. Now BRAKER3 outputs are not saved by default [#53](https://github.com/PlantandFoodResearch/pangene/issues/53) and saved under `etc` folder when enabled
+10. Removed `local` profile. Local executor is the default when no executor is specified. Therefore, the `local` profile was not needed.
 
 ## 0.3.3 - [18-Jun-2024]
 

diff --git a/conf/base.config b/conf/base.config
@@ -1,34 +1,3 @@
-profiles {
-    pfr {
-        process {
-            executor        = 'slurm'
-        }
-
-        apptainer {
-            envWhitelist    = 'APPTAINER_BINDPATH,APPTAINER_BIND'
-            cacheDir        = "/workspace/pangene/singularity"
-        }
-    }
-
-    local {
-        process {
-            executor        = 'local'
-        }
-    }
-
-    apptainer {
-        apptainer.enabled   = true
-        apptainer.autoMounts= true
-        apptainer.registry  = 'quay.io'
-    }
-
-    docker {
-        docker.enabled      = true
-        docker.runOptions   = '-u $(id -u):$(id -g) --platform=linux/amd64'
-        docker.registry     = 'quay.io'
-    }
-}
-
 process {
 
     cpus                    = { check_max( 1    * task.attempt, 'cpus'   ) }

diff --git a/conf/modules.config b/conf/modules.config
@@ -146,7 +146,7 @@ process { // SUBWORKFLOW: FASTA_BRAKER3
         ].flatten().unique(false).join(' ').trim()
         ext.prefix = { "${meta.id}" }
         publishDir = [
-            path: { "${params.outdir}/braker/" },
+            path: { "${params.outdir}/etc/braker/" },
             mode: "copy",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.braker_save_outputs
@@ -335,7 +335,7 @@ process { // Universal
 
     withName: SAVE_MARKED_GFF3 {
         publishDir = [
-            path: { "${params.outdir}/splicing_marked" },
+            path: { "${params.outdir}/etc/splicing_marked" },
             mode: "copy",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]

diff --git a/conf/test.config b/conf/test.config
@@ -0,0 +1,7 @@
+params {
+    input                   = "${projectDir}/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' // Added for faster test execution! Do not use with actual data!
+    busco_lineage_datasets  = 'eudicots_odb10'
+}
diff --git a/docs/parameters.md b/docs/parameters.md
@@ -7,9 +7,9 @@ A NextFlow pipeline for pan-genome annotation
 | Parameter                 | Description                                                                                              | Type      | Default   | Required | Hidden |
 | ------------------------- | -------------------------------------------------------------------------------------------------------- | --------- | --------- | -------- | ------ |
 | `input`                   | Target assemblies listed in a CSV sheet                                                                  | `string`  |           | True     |        |
-| `protein_evidence`        | Protein evidence provided as fasta files listed in a text sheet                                          | `string`  |           | True     |        |
-| `eggnogmapper_db_dir`     | Eggnogmapper database directory                                                                          | `string`  |           | True     |        |
-| `eggnogmapper_tax_scope`  | Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1 | `integer` |           | True     |        |
+| `protein_evidence`        | Protein evidence provided as a fasta file or multiple fasta files listed in a plain txt file             | `string`  |           | True     |        |
+| `eggnogmapper_db_dir`     | Eggnogmapper database directory                                                                          | `string`  |           |          |        |
+| `eggnogmapper_tax_scope`  | Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1 | `integer` | 1         |          |        |
 | `rna_evidence`            | FASTQ/BAM samples listed in a CSV sheet                                                                  | `string`  |           |          |        |
 | `liftoff_annotations`     | Reference annotations listed in a CSV sheet                                                              | `string`  |           |          |        |
 | `orthofinder_annotations` | Additional annotations for orthology listed in a CSV sheet                                               | `string`  |           |          |        |

diff --git a/local_pangene b/local_pangene
@@ -14,8 +14,10 @@ F_BOLD="\033[1m"
 
 nextflow run \
     main.nf \
-    -profile local,docker \
+    -profile docker,test \
     -resume \
     $stub \
-    -params-file pangene-test/params.json \
+    --max_cpus 8 \
+    --max_memory '32.GB' \
+    --eggnogmapper_tax_scope 33090 \
     --eggnogmapper_db_dir ../dbs/emapperdb/5.0.2
diff --git a/modules/local/utils.nf b/modules/local/utils.nf
@@ -4,7 +4,7 @@ def idFromFileName(fileName) {
         ).replaceFirst(
             /\.f(ast)?q$/, ''
         ).replaceFirst(
-            /\.f(asta|sa|a|as|aa)?$/, ''
+            /\.f(asta|sa|a|as|aa|na)?$/, ''
         ).replaceFirst(
             /\.gff(3)?$/, ''
         ).replaceFirst(

diff --git a/nextflow.config b/nextflow.config
@@ -1,11 +1,9 @@
-includeConfig './conf/base.config'
-
 params {
     // Input/output options
     input                       = null
     protein_evidence            = null
     eggnogmapper_db_dir         = null
-    eggnogmapper_tax_scope      = null
+    eggnogmapper_tax_scope      = 1
     rna_evidence                = null
     liftoff_annotations         = null
     orthofinder_annotations     = null
@@ -21,20 +19,20 @@ params {
     skip_fastqc                 = false
     skip_fastp                  = false
     min_trimmed_reads           = 10000
-    extra_fastp_args            = ""
+    extra_fastp_args            = null
     save_trimmed                = false
     remove_ribo_rna             = false
     save_non_ribo_reads         = false
     ribo_database_manifest      = "${projectDir}/assets/rrna-db-defaults.txt"
 
     // RNAseq alignment options
     star_max_intron_length      = 16000
-    star_align_extra_args       = ""
+    star_align_extra_args       = null
     star_save_outputs           = false
     save_cat_bam                = false
 
     // Annotation options
-    braker_extra_args           = ""
+    braker_extra_args           = null
     braker_save_outputs         = false
     liftoff_coverage            = 0.9
     liftoff_identity            = 0.9
@@ -59,15 +57,26 @@ params {
     validationS3PathCheck       = true
 }
 
-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'
-    doi                         = ''
+includeConfig './conf/base.config'
+
+profiles {
+    apptainer {
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        apptainer.registry      = 'quay.io'
+    }
+
+    docker {
+        docker.enabled          = true
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.registry         = 'quay.io'
+    }
+
+    test { includeConfig 'conf/test.config' }
+}
+
+plugins {
+    id '[email protected]'
 }
 
 def trace_timestamp             = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
@@ -84,8 +93,15 @@ trace {
     file                        = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 
-plugins {
-    id '[email protected]'
+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/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "",
-            "required": ["input", "protein_evidence", "eggnogmapper_db_dir", "eggnogmapper_tax_scope", "outdir"],
+            "required": ["input", "protein_evidence", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -23,9 +23,9 @@
                 },
                 "protein_evidence": {
                     "type": "string",
-                    "description": "Protein evidence provided as fasta files listed in a text sheet",
+                    "description": "Protein evidence provided as a fasta file or multiple fasta files listed in a plain txt file",
                     "format": "file-path",
-                    "mimetype": "text/txt",
+                    "pattern": "^\\S+\\.(txt|fa|faa|fna|fsa|fas|fasta)(\\.gz)?$",
                     "fa_icon": "far fa-file-alt"
                 },
                 "eggnogmapper_db_dir": {
@@ -36,7 +36,8 @@
                 "eggnogmapper_tax_scope": {
                     "type": "integer",
                     "description": "Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1",
-                    "minimum": 0
+                    "minimum": 1,
+                    "default": 1
                 },
                 "rna_evidence": {
                     "type": "string",

diff --git a/subworkflows/local/gff_eggnogmapper.nf b/subworkflows/local/gff_eggnogmapper.nf
@@ -24,7 +24,9 @@ workflow GFF_EGGNOGMAPPER {
     ch_versions                 = ch_versions.mix(GFF2FASTA_FOR_EGGNOGMAPPER.out.versions.first())
 
 
-    ch_eggnogmapper_inputs      = ch_gffread_fasta
+    ch_eggnogmapper_inputs      = ! db_folder
+                                ? Channel.empty()
+                                : ch_gffread_fasta
                                 | combine(Channel.fromPath(db_folder))
 
     EGGNOGMAPPER(

diff --git a/subworkflows/local/gff_store.nf b/subworkflows/local/gff_store.nf
@@ -8,12 +8,15 @@ workflow GFF_STORE {
     ch_target_gff               // [ meta, gff ]
     ch_eggnogmapper_annotations // [ meta, annotations ]
     ch_fasta                    // [ meta, fasta ]
+    val_describe_gff            // val(true|false)
 
     main:
     ch_versions                 = Channel.empty()
 
     // COLLECTFILE: Add eggnogmapper hits to gff
-    ch_described_gff            = ch_target_gff
+    ch_described_gff            = ! val_describe_gff
+                                ? Channel.empty()
+                                : ch_target_gff
                                 | join(ch_eggnogmapper_annotations)
                                 | map { meta, gff, annotations ->
                                     def tx_annotations  = annotations.readLines()
@@ -109,7 +112,11 @@ workflow GFF_STORE {
                                 }
 
     // MODULE: GT_GFF3 as FINAL_GFF_CHECK
-    FINAL_GFF_CHECK ( ch_described_gff )
+    ch_final_check_input        = val_describe_gff
+                                ? ch_described_gff
+                                : ch_target_gff
+
+    FINAL_GFF_CHECK ( ch_final_check_input )
 
     ch_final_gff                = FINAL_GFF_CHECK.out.gt_gff3
     ch_versions                 = ch_versions.mix(FINAL_GFF_CHECK.out.versions.first())

diff --git a/subworkflows/local/purge_nohit_models.nf b/subworkflows/local/purge_nohit_models.nf
@@ -60,6 +60,11 @@ workflow PURGE_NOHIT_MODELS {
     ch_versions                 = ch_versions.mix(AGAT_SPFILTERFEATUREFROMKILLLIST.out.versions.first())
 
     emit:
-    purged_gff                  = ch_target_purged_gff.mix(val_purge_nohits ? Channel.empty() : ch_target_gff)
+    purged_gff                  = ch_target_purged_gff
+                                | mix(
+                                    val_purge_nohits
+                                    ? Channel.empty()
+                                    : ch_target_gff
+                                )
     versions                    = ch_versions   // [ versions.yml ]
 }
diff --git a/tests/minimal/assemblysheet.csv b/tests/minimal/assemblysheet.csv
@@ -0,0 +1,2 @@
+tag,fasta,is_masked
+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
@@ -0,0 +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",
+    "busco_lineage_datasets": "eudicots_odb10"
+}
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		tag,fasta,is_masked
		a_thaliana,https://raw.githubusercontent.com/Gaius-Augustus/BRAKER/f58479fe5bb13a9e51c3ca09cb9e137cab3b8471/example/genome.fa,yes