From 294c4a2fc28cb30ccbe792ecf22318413d5b04b6 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Wed, 28 Feb 2024 10:51:45 +1300
Subject: [PATCH] Fixed linting issues

---
 lib/WorkflowAssemblyqc.groovy | 21 +++++++--------------
 modules/local/createreport.nf | 20 ++++++++++++++++++--
 2 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/lib/WorkflowAssemblyqc.groovy b/lib/WorkflowAssemblyqc.groovy
index 7a11ebe..e5b7798 100755
--- a/lib/WorkflowAssemblyqc.groovy
+++ b/lib/WorkflowAssemblyqc.groovy
@@ -14,44 +14,37 @@ class WorkflowAssemblyqc {
     public static void initialise(params, log) {
         // Check for ncbi_fcs_adaptor_empire
         if (!params.ncbi_fcs_adaptor_skip && !params.ncbi_fcs_adaptor_empire) {
-            log.error('ncbi_fcs_adaptor_empire must be provided when executing NCBI FCS Adaptor')
-            System.exit(1)
+            Nextflow.error('ncbi_fcs_adaptor_empire must be provided when executing NCBI FCS Adaptor')
         }
 
         // Check for ncbi_fcs_gx_tax_id
         if (!params.ncbi_fcs_gx_skip && !params.ncbi_fcs_gx_tax_id) {
-            log.error('ncbi_fcs_gx_tax_id must be provided when executing NCBI FCS GX')
-            System.exit(1)
+            Nextflow.error('ncbi_fcs_gx_tax_id must be provided when executing NCBI FCS GX')
         }
 
         // Check for ncbi_fcs_gx_db_path
         if (!params.ncbi_fcs_gx_skip && !params.ncbi_fcs_gx_db_path) {
-            log.error('ncbi_fcs_gx_db_path must be provided when executing NCBI FCS GX')
-            System.exit(1)
+            Nextflow.error('ncbi_fcs_gx_db_path must be provided when executing NCBI FCS GX')
         }
 
         // Check for busco_mode
         if (!params.busco_skip && !params.busco_mode) {
-            log.error("busco_mode must be provided when executing BUSCO")
-            System.exit(1)
+            Nextflow.error("busco_mode must be provided when executing BUSCO")
         }
 
         // Check for busco_lineage_datasets
         if (!params.busco_skip && !params.busco_lineage_datasets) {
-            log.error('busco_lineage_datasets must be provided when executing BUSCO')
-            System.exit(1)
+            Nextflow.error('busco_lineage_datasets must be provided when executing BUSCO')
         }
 
         // Check for tidk_repeat_seq
         if (!params.tidk_skip && !params.tidk_repeat_seq) {
-            log.error('tidk_repeat_seq must be provided when executing TIDK')
-            System.exit(1)
+            Nextflow.error('tidk_repeat_seq must be provided when executing TIDK')
         }
 
         // Check for kraken2_db_path
         if (!params.kraken2_skip && !params.kraken2_db_path) {
-            log.error('kraken2_db_path must be provided when executing Kraken2')
-            System.exit(1)
+            Nextflow.error('kraken2_db_path must be provided when executing Kraken2')
         }
     }
 
diff --git a/modules/local/createreport.nf b/modules/local/createreport.nf
index 41c69b2..29ea765 100644
--- a/modules/local/createreport.nf
+++ b/modules/local/createreport.nf
@@ -21,18 +21,34 @@ process CREATEREPORT {
     val params_json
 
     output:
-    path 'report.html'
-    path 'report.json'
+    path 'report.html'  , emit: html
+    path 'report.json'  , emit: json
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
     """
     echo -n '$params_json' > params_json.json
     assemblyqc.py > report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | tr -d 'Python[:space:]')
+        pandas: \$(python -c "import pandas; print(pandas.__version__)")
+    END_VERSIONS
     """
 
     stub:
     """
     touch report.html
     touch report.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | tr -d 'Python[:space:]')
+        pandas: \$(python -c "import pandas; print(pandas.__version__)")
+    END_VERSIONS
     """
 }