From 49af33f68ea7ab216db898adc24fe2489a8c2f03 Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Tue, 29 Nov 2022 11:07:29 +0100
Subject: [PATCH] Include NCBI_id, read counts and mgc arguments in motus

---
 conf/modules.config    | 1 +
 conf/test_motus.config | 3 +++
 nextflow.config        | 3 +++
 3 files changed, 7 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index f9d51d8..5c35525 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -446,6 +446,7 @@ process {
     }
 
     withName: MOTUS_PROFILE {
+        ext.args = { [ params.save_ncbi_id ? "-p" : "", params.save_read_counts ? "-c" : "", params.save_mgc_counts ?  "-M ${task.ext.prefix}.mgc" : "" ].join(',').replaceAll(','," ") }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/motus/${meta.db_name}/" },
diff --git a/conf/test_motus.config b/conf/test_motus.config
index d167b94..70681dd 100644
--- a/conf/test_motus.config
+++ b/conf/test_motus.config
@@ -39,5 +39,8 @@ params {
     run_centrifuge                        = false
     run_diamond                           = false
     run_motus                             = true
+    save_mgc_counts                       = true
+    save_ncbi_id                          = true
+    save_read_counts                      = true
     run_profile_standardisation           = true
 }
diff --git a/nextflow.config b/nextflow.config
index c59d433..91875b2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -140,6 +140,9 @@ params {
 
     // mOTUs
     run_motus                  = false
+    save_mgc_counts            = false
+    save_ncbi_id               = false
+    save_read_counts           = false
 
     // krona
     run_krona                  = false