From 3702329954625e8beafb2a9de9c25545feac0554 Mon Sep 17 00:00:00 2001
From: "Diego Alvarez S." <dialvarezs@gmail.com>
Date: Thu, 31 Oct 2024 18:22:22 -0300
Subject: [PATCH] Final touches

---
 conf/modules.config          |  4 ++--
 subworkflows/local/bin_qc.nf | 36 ++++++++++++++++++++----------------
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index b0a58c42..63e66adf 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -368,8 +368,8 @@ process {
         ]
     }
 
-    withName: COMBINE_CHECKM_TSV {
-        ext.prefix = { params.binqc_tool == "checkm" ? "checkm_summary" : "checkm2_summary" }
+    withName: COMBINE_BINQC_TSV {
+        ext.prefix = { "${params.binqc_tool}_summary" }
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC" },
             mode: params.publish_dir_mode,
diff --git a/subworkflows/local/bin_qc.nf b/subworkflows/local/bin_qc.nf
index 4aa9b50a..e7f7d3fb 100644
--- a/subworkflows/local/bin_qc.nf
+++ b/subworkflows/local/bin_qc.nf
@@ -2,14 +2,14 @@
  * BUSCO/CheckM/CheckM2: Quantitative measures for the assessment of genome assembly
  */
 
-include { BUSCO_DB_PREPARATION  } from '../../modules/local/busco_db_preparation'
-include { BUSCO                 } from '../../modules/local/busco'
-include { BUSCO_SAVE_DOWNLOAD   } from '../../modules/local/busco_save_download'
-include { BUSCO_SUMMARY         } from '../../modules/local/busco_summary'
-include { CHECKM_QA             } from '../../modules/nf-core/checkm/qa/main'
-include { CHECKM_LINEAGEWF      } from '../../modules/nf-core/checkm/lineagewf/main'
-include { CHECKM2_PREDICT       } from '../../modules/nf-core/checkm2/predict/main'
-include { COMBINE_TSV           } from '../../modules/local/combine_tsv'
+include { BUSCO_DB_PREPARATION              } from '../../modules/local/busco_db_preparation'
+include { BUSCO                             } from '../../modules/local/busco'
+include { BUSCO_SAVE_DOWNLOAD               } from '../../modules/local/busco_save_download'
+include { BUSCO_SUMMARY                     } from '../../modules/local/busco_summary'
+include { CHECKM_QA                         } from '../../modules/nf-core/checkm/qa/main'
+include { CHECKM_LINEAGEWF                  } from '../../modules/nf-core/checkm/lineagewf/main'
+include { CHECKM2_PREDICT                   } from '../../modules/nf-core/checkm2/predict/main'
+include { COMBINE_TSV as COMBINE_BINQC_TSV  } from '../../modules/local/combine_tsv'
 
 workflow BIN_QC {
     take:
@@ -20,6 +20,8 @@ workflow BIN_QC {
 
     main:
     ch_versions = Channel.empty()
+    multiqc_reports = []
+    checkm_tsv = []
 
     if (params.binqc_tool == "busco") {
         // BUSCO workflow
@@ -76,12 +78,13 @@ workflow BIN_QC {
     else if (params.binqc_tool == "checkm") {
         // CheckM workflow
         ch_bins_for_checkmlineagewf = bins
+            .groupTuple()
             .filter { meta, _bins ->
                     meta.domain != "eukarya"
                 }
             .multiMap { meta, fa ->
                 reads: [meta, fa]
-                ext: fa.extension.unique().join("")
+                ext: fa.extension.unique().join("")  // the pipeline ensures that all bins will have the same extension
             }
 
         CHECKM_LINEAGEWF(ch_bins_for_checkmlineagewf.reads, ch_bins_for_checkmlineagewf.ext, checkm_db)
@@ -95,24 +98,25 @@ workflow BIN_QC {
 
         CHECKM_QA(ch_checkmqa_input, [])
 
-        COMBINE_TSV(CHECKM_QA.out.output.map { it[1] }.collect())
+        COMBINE_BINQC_TSV(CHECKM_QA.out.output.map { it[1] }.collect())
 
-        summary = COMBINE_TSV.out.combined
+        summary = COMBINE_BINQC_TSV.out.combined
         ch_versions = ch_versions.mix(CHECKM_QA.out.versions.first())
+        checkm_tsv = CHECKM_QA.out.output
     }
     else if (params.binqc_tool == "checkm2") {
         // CheckM2 workflow
-        CHECKM2_PREDICT(bins, checkm2_db)
+        CHECKM2_PREDICT(bins.groupTuple(), checkm2_db)
 
-        COMBINE_TSV(CHECKM2_PREDICT.out.checkm2_tsv.map { it[1] }.collect())
+        COMBINE_BINQC_TSV(CHECKM2_PREDICT.out.checkm2_tsv.map { it[1] }.collect())
 
-        summary = COMBINE_TSV.out.combined
+        summary = COMBINE_BINQC_TSV.out.combined
         ch_versions = ch_versions.mix(CHECKM2_PREDICT.out.versions.first())
     }
 
     emit:
     summary     = summary
-    checkm_tsv  = params.binqc_tool == "checkm" ? CHECKM_QA.out.output : []
-    multiqc     = params.binqc_tool == "busco" ? multiqc_reports : []
+    checkm_tsv  = checkm_tsv
+    multiqc     = multiqc_reports
     versions    = ch_versions
 }