Allow num_chains to be set in the config

modules/msk/phylowgs/multievolve/environment.yml

@@ -1,9 +1,6 @@
 ---
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "phylowgs_multievolve"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "PHYLOWGS"
+  - "PHYLOWGS=NA"

modules/msk/phylowgs/multievolve/main.nf

@@ -19,13 +19,11 @@ process PHYLOWGS_MULTIEVOLVE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def threads = task.cpus * 2
 
     """
     python2 \\
         /usr/bin/multievolve.py  \\
         ${args} \\
-        --num-chains ${threads} \\
         --ssms ${ssm_data} \\
         --cnvs ${cnv_data}
 

modules/msk/phylowgs/multievolve/meta.yml

@@ -1,5 +1,4 @@
 ---
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "phylowgs_multievolve"
 description: Create trees from input from phylowgs_createinput
 keywords:
@@ -13,34 +12,36 @@ tools:
       tool_dev_url: "https://github.com/mskcc/phylowgs"
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  - cnv_data:
-      type: file
-      description: copy number input data from phylowgs_createinput
-      pattern: "*.{txt}"
-  - ssm_data:
-      type: file
-      description: mutation input data from phylowgs_createinput
-      pattern: "*.{txt}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - cnv_data:
+        type: file
+        description: copy number input data from phylowgs_createinput
+        pattern: "*.{txt}"
+    - ssm_data:
+        type: file
+        description: mutation input data from phylowgs_createinput
+        pattern: "*.{txt}"
 
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
   - trees:
-      type: file
-      description: Zip file containing the completed trees
-      pattern: "trees.zip"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - chains/trees.zip:
+          type: file
+          description: Zip file containing the completed trees
+          pattern: "trees.zip"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 
 authors:
   - "@nikhil"

modules/msk/phylowgs/multievolve/tests/nextflow.config

@@ -5,6 +5,6 @@ params {
 process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     withName: 'PHYLOWGS_MULTIEVOLVE' {
-        ext.args = '--burnin-samples 2 --mcmc-samples 2'
+        ext.args = '--num-chains 2 --burnin-samples 2 --mcmc-samples 2'
     }
 }