Cleanup

nf-core · Oct 31, 2024 · 38ce756 · 38ce756
1 parent 0ebab07
commit 38ce756
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Showing 4 changed files with 11 additions and 101 deletions.
diff --git a/subworkflows/local/bin_qc.nf b/subworkflows/local/bin_qc.nf
@@ -47,26 +47,22 @@ workflow BIN_QC {
             // Set BUSCO database to empty to allow for --auto-lineage
             ch_db_for_busco = Channel
                 .of([])
-                .map { empty_db -> [[lineage: ''], []] }
+                .map { _empty_db -> [[lineage: ''], []] }
                 .collect()
         }
 
         if (params.save_busco_db) {
             // publish files downloaded by Busco
             ch_downloads = BUSCO.out.busco_downloads
                 .groupTuple()
-                .map { lin, downloads -> downloads[0] }
+                .map { _lin, downloads -> downloads[0] }
                 .toSortedList()
                 .flatten()
             BUSCO_SAVE_DOWNLOAD(ch_downloads)
         }
 
         BUSCO(bins, ch_db_for_busco)
 
-        // busco_summary_domain = BUSCO.out.summary_domain.collect()
-        // busco_summary_specific = BUSCO.out.summary_specific.collect()
-        // busco_failed_bin = BUSCO.out.failed_bin.collect()
-
         BUSCO_SUMMARY(
             BUSCO.out.summary_domain.map { it[1] }.collect().ifEmpty([]),
             BUSCO.out.summary_specific.map { it[1] }.collect().ifEmpty([]),
@@ -80,7 +76,7 @@ workflow BIN_QC {
     else if (params.binqc_tool == "checkm") {
         // CheckM workflow
         ch_bins_for_checkmlineagewf = bins
-            .filter { meta, bin ->
+            .filter { meta, _bins ->
                     meta.domain != "eukarya"
                 }
             .multiMap { meta, fa ->

diff --git a/subworkflows/local/busco_qc.nf b/subworkflows/local/busco_qc.nf
diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
@@ -9,8 +9,7 @@ include { GTDBTK_SUMMARY        } from '../../modules/local/gtdbtk_summary'
 workflow GTDBTK {
     take:
     bins              // channel: [ val(meta), [bins] ]
-    busco_summary     // channel: path
-    checkm_summary    // channel: path
+    bin_qc_summary    // channel: path
     gtdb              // channel: path
     gtdb_mash         // channel: path
 
@@ -19,7 +18,7 @@ workflow GTDBTK {
     ch_bin_metrics = Channel.empty()
     if ( params.binqc_tool == 'busco' ){
         // Collect completeness and contamination metrics from busco summary
-        ch_bin_metrics = busco_summary
+        ch_bin_metrics = bin_qc_summary
             .splitCsv(header: true, sep: '\t')
             .map { row ->
                         def completeness  = -1
@@ -41,7 +40,7 @@ workflow GTDBTK {
         // Collect completeness and contamination metrics from CheckM/CheckM2 summary
         bin_name = params.binqc_tool == 'checkm' ? 'Bin Id' : 'Name'
 
-        ch_bin_metrics = checkm_summary
+        ch_bin_metrics = bin_qc_summary
             .splitCsv(header: true, sep: '\t')
             .map { row ->
                         def completeness  = Double.parseDouble(row.'Completeness')

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -649,9 +649,7 @@ workflow MAG {
     ================================================================================
     */
 
-    ch_busco_summary = Channel.empty()
-    ch_checkm_summary = Channel.empty()
-    ch_checkm2_summary = Channel.empty()
+    bin_qc_summary = Channel.empty()
 
     if (!params.skip_binning || params.ancient_dna) {
         BINNING_PREPARATION(
@@ -803,10 +801,11 @@ workflow MAG {
             ch_busco_db
         )
 
+        bin_qc_summary = BIN_QC.out.summary
         ch_versions = ch_versions.mix(BIN_QC.out.versions)
 
         if (params.run_gunc) {
-            ch_input_bins_for_gunc = ch_input_for_postbinning.filter { meta, bins ->
+            ch_input_bins_for_gunc = ch_input_for_postbinning.filter { meta, _bins ->
                 meta.domain != "eukarya"
             }
 
@@ -887,8 +886,7 @@ workflow MAG {
 
                 GTDBTK(
                     ch_gtdb_bins,
-                    ch_busco_summary,
-                    ch_checkm_summary,
+                    bin_qc_summary,
                     gtdb,
                     gtdb_mash
                 )
@@ -903,7 +901,7 @@ workflow MAG {
         if ((!params.skip_binqc) || !params.skip_quast || !params.skip_gtdbtk) {
             BIN_SUMMARY(
                 ch_input_for_binsummary,
-                params.binqc_tool == "busco" ? ch_busco_summary.ifEmpty([]) : ch_checkm_summary.ifEmpty([]),
+                bin_qc_summary.ifEmpty([]),
                 ch_quast_bins_summary.ifEmpty([]),
                 ch_gtdbtk_summary.ifEmpty([]),
                 ch_cat_global_summary.ifEmpty([])