feat: Add evolCCM entry (#174)

* feat: Add evolCCM entry Signed-off-by: jvfe <[email protected]> * refactor: Keep mandatory param check to workflows * chore: Update schema * refactor: Remove input_sample_table check from lib --------- Signed-off-by: jvfe <[email protected]>
beiko-lab · Nov 5, 2023 · 8bdad86 · 8bdad86
1 parent eb265b1
commit 8bdad86
Show file tree

Hide file tree

Showing 6 changed files with 26 additions and 14 deletions.
diff --git a/docs/params.md b/docs/params.md
@@ -95,8 +95,9 @@ Parameters for the recombination subworkflow
 | `min_branch_length` | Minimum rSPR branch length | `integer` | 0 |  |  |
 | `max_support_threshold` | Maximum rSPR support threshold | `number` | 0.7 |  |  |
 | `max_approx_rspr` | Maximum approximate rSPR distance for filtering | `integer` | -1 |  |  |
-| `core_gene_tree` | Core (or reference) genome tree. Used in the rSPR entry. | `string` |  |  |  |
+| `core_gene_tree` | Core (or reference) genome tree. Used in the rSPR and evolCCM entries. | `string` |  |  |  |
 | `concatenated_annotation` | TSV table of annotations for all genomes. Such as the ones generated by Bakta or Prokka in ARETE. | `string` |  |  |  |
+| `feature_profile` | Feature profile TSV (A presence-absence matrix). Used in the evolCCM entry. | `string` |  |  |  |
 
 ## Institutional config options
 

diff --git a/lib/WorkflowArete.groovy b/lib/WorkflowArete.groovy
@@ -66,11 +66,6 @@ class WorkflowArete {
         // Check the hostnames against configured profiles
         NfcoreTemplate.hostName(workflow, params, log)
 
-        // Check input has been provided
-        if (!params.input_sample_table) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input_sample_table samplesheet.csv'"
-            System.exit(1)
-        }
     }
 
     //

diff --git a/main.nf b/main.nf
@@ -38,6 +38,7 @@ include { PHYLO } from './workflows/arete'
 include { QUALITYCHECK } from './workflows/arete'
 include { POPPUNK } from './workflows/arete'
 include { RUN_RSPR } from './workflows/arete'
+include { RUN_EVOLCCM } from './workflows/arete'
 
 
 //
@@ -72,6 +73,10 @@ workflow poppunk {
 workflow rspr {
     RUN_RSPR()
 }
+
+workflow evolccm {
+    RUN_EVOLCCM()
+}
 /*
 ========================================================================================
     RUN ALL WORKFLOWS

diff --git a/nextflow.config b/nextflow.config
@@ -66,9 +66,10 @@ params {
     max_support_threshold      = 0.7
     max_approx_rspr            = -1
 
-    // rSPR entry
+    // rSPR/evolCCM entries
     core_gene_tree             = null
     concatenated_annotation    = null
+    feature_profile            = null
 
     // MultiQC options
     multiqc_config             = null

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input_sample_table"],
+            "required": [],
             "properties": {
                 "input_sample_table": {
                     "type": "string",
@@ -217,7 +217,7 @@
                 },
                 "accessory_similarity": {
                     "type": "number",
-                    "default": 99,
+                    "default": 99.0,
                     "fa_icon": "far fa-clone",
                     "description": "Similarity threshold for accessory genes"
                 }
@@ -282,11 +282,15 @@
                 },
                 "core_gene_tree": {
                     "type": "string",
-                    "description": "Core (or reference) genome tree. Used in the rSPR entry."
+                    "description": "Core (or reference) genome tree. Used in the rSPR and evolCCM entries."
                 },
                 "concatenated_annotation": {
                     "type": "string",
                     "description": "TSV table of annotations for all genomes. Such as the ones generated by Bakta or Prokka in ARETE."
+                },
+                "feature_profile": {
+                    "type": "string",
+                    "description": "Feature profile TSV (A presence-absence matrix). Used in the evolCCM entry."
                 }
             },
             "fa_icon": "fas fa-bezier-curve"

diff --git a/workflows/arete.nf b/workflows/arete.nf
@@ -11,10 +11,6 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 def checkPathParamList = [ params.input_sample_table, params.multiqc_config, params.reference_genome ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
-// Check mandatory parameters
-if (params.input_sample_table) { ch_input = file(params.input_sample_table) } else { exit 1, 'Input samplesheet not specified!' }
-
-
 /*
 ========================================================================================
     CONFIG FILES
@@ -609,6 +605,16 @@ workflow RUN_RSPR {
     )
 }
 
+workflow RUN_EVOLCCM {
+    if (params.core_gene_tree) { ch_core = file(params.core_gene_tree) } else { exit 1, 'Core tree not specified!' }
+    if (params.feature_profile) { ch_input = file(params.feature_profile) } else { exit 1, 'Input feature profile not specified!' }
+
+    EVOLCCM (
+        ch_core,
+        ch_input
+    )
+}
+
 /*
 ========================================================================================
     COMPLETION EMAIL AND SUMMARY