From d176fcee3f4833d5c1b7bd888a3288f79f4afc73 Mon Sep 17 00:00:00 2001
From: "Diego Alvarez S." <dialvarezs@gmail.com>
Date: Thu, 5 Dec 2024 10:37:11 -0300
Subject: [PATCH] Handle skip_binqc properly

---
 subworkflows/local/bin_qc.nf | 4 ++--
 workflows/mag.nf             | 8 +++++---
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/bin_qc.nf b/subworkflows/local/bin_qc.nf
index e78b7b3b..ada34149 100644
--- a/subworkflows/local/bin_qc.nf
+++ b/subworkflows/local/bin_qc.nf
@@ -44,7 +44,7 @@ workflow BIN_QC {
     if (params.checkm_db) {
         ch_checkm_db = file(params.checkm_db, checkIfExists: true)
     }
-    else if (!params.skip_binqc && params.binqc_tool == 'checkm') {
+    else if (params.binqc_tool == 'checkm') {
         ARIA2_UNTAR(params.checkm_download_url)
         ch_checkm_db = ARIA2_UNTAR.out.downloaded_file
     }
@@ -55,7 +55,7 @@ workflow BIN_QC {
     if (params.checkm2_db) {
         ch_checkm2_db = [[:], file(params.checkm2_db, checkIfExists: true)]
     }
-    else if (!params.skip_binqc && params.binqc_tool == 'checkm2') {
+    else if (params.binqc_tool == 'checkm2') {
         CHECKM2_DATABASEDOWNLOAD(params.checkm2_db_version)
         ch_checkm2_db = CHECKM2_DATABASEDOWNLOAD.out.database
     }
diff --git a/workflows/mag.nf b/workflows/mag.nf
index b269a19f..1ef0e52b 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -615,10 +615,12 @@ workflow MAG {
         * Bin QC subworkflows: for checking bin completeness with either BUSCO, CHECKM, CHECKM2, and/or GUNC
         */
 
-        BIN_QC(ch_input_for_postbinning)
+        if (!params.skip_binqc) {
+            BIN_QC(ch_input_for_postbinning)
 
-        ch_bin_qc_summary = BIN_QC.out.qc_summary
-        ch_versions = ch_versions.mix(BIN_QC.out.versions)
+            ch_bin_qc_summary = BIN_QC.out.qc_summary
+            ch_versions = ch_versions.mix(BIN_QC.out.versions)
+        }
 
         ch_quast_bins_summary = Channel.empty()
         if (!params.skip_quast) {