Handle skip_binqc properly

nf-core · Dec 5, 2024 · d176fce · d176fce
1 parent f75e9c4
commit d176fce
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git 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
@@ -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) {