From 64a13ef96ba904cec5cf6a832e16ee9ea7ea30b2 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 21 Jan 2025 11:47:24 +0100
Subject: [PATCH] Use channel empty when no phix reference supplied because
 skipping

---
 CHANGELOG.md     |  2 ++
 workflows/mag.nf | 45 ++++++++++++++++++++++++---------------------
 2 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 004375b5..1679a584 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#748](https://github.com/nf-core/mag/pull/748) - Fix broken phix reference channel when skipping phix removal (reported by @amizeranschi, fix by @muabnezor)
+
 ### `Dependencies`
 
 ### `Dependencies`
diff --git a/workflows/mag.nf b/workflows/mag.nf
index de353a40..3ad2800b 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -63,7 +63,7 @@ include { COMBINE_TSV as COMBINE_SUMMARY_TSV                    } from '../modul
 
 workflow MAG {
     take:
-    ch_raw_short_reads // channel: samplesheet read in from --input
+    ch_raw_short_reads  // channel: samplesheet read in from --input
     ch_raw_long_reads
     ch_input_assemblies
 
@@ -113,10 +113,14 @@ workflow MAG {
     if (!params.keep_phix) {
         ch_phix_db_file = Channel.value(file("${params.phix_reference}"))
     }
+    else {
+        ch_phix_db_file = Channel.empty()
+    }
 
     if (!params.keep_lambda) {
-        ch_lambda_db = Channel.value(file( "${params.lambda_reference}" ))
-    } else {
+        ch_lambda_db = Channel.value(file("${params.lambda_reference}"))
+    }
+    else {
         ch_lambda_db = Channel.empty()
     }
 
@@ -162,14 +166,13 @@ workflow MAG {
             ch_raw_short_reads,
             ch_host_fasta,
             ch_phix_db_file,
-            ch_metaeuk_db
+            ch_metaeuk_db,
         )
 
         ch_versions = ch_versions.mix(SHORTREAD_PREPROCESSING.out.versions)
         ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.multiqc_files.collect { it[1] }.ifEmpty([]))
         ch_short_reads = SHORTREAD_PREPROCESSING.out.short_reads
         ch_short_reads_assembly = SHORTREAD_PREPROCESSING.out.short_reads_assembly
-
     }
     else {
         ch_short_reads = ch_raw_short_reads.map { meta, reads ->
@@ -187,7 +190,7 @@ workflow MAG {
     LONGREAD_PREPROCESSING(
         ch_raw_long_reads,
         ch_short_reads,
-        ch_lambda_db
+        ch_lambda_db,
     )
 
     ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions)
@@ -218,7 +221,7 @@ workflow MAG {
         ch_short_reads,
         ch_db_for_centrifuge,
         false,
-        false
+        false,
     )
     ch_versions = ch_versions.mix(CENTRIFUGE_CENTRIFUGE.out.versions.first())
 
@@ -255,7 +258,7 @@ workflow MAG {
 
     KRAKEN2(
         ch_short_reads,
-        ch_db_for_kraken2
+        ch_db_for_kraken2,
     )
     ch_versions = ch_versions.mix(KRAKEN2.out.versions.first())
 
@@ -287,7 +290,7 @@ workflow MAG {
 
         KRONA_KTIMPORTTAXONOMY(
             ch_tax_classifications,
-            ch_krona_db
+            ch_krona_db,
         )
         ch_versions = ch_versions.mix(KRONA_KTIMPORTTAXONOMY.out.versions.first())
     }
@@ -450,7 +453,7 @@ workflow MAG {
     if (!params.skip_prodigal) {
         PRODIGAL(
             ch_assemblies,
-            'gff'
+            'gff',
         )
         ch_versions = ch_versions.mix(PRODIGAL.out.versions.first())
     }
@@ -477,7 +480,7 @@ workflow MAG {
     if (!params.skip_binning || params.ancient_dna) {
         BINNING_PREPARATION(
             ch_assemblies,
-            ch_short_reads
+            ch_short_reads,
         )
         ch_versions = ch_versions.mix(BINNING_PREPARATION.out.bowtie2_version.first())
     }
@@ -505,13 +508,13 @@ workflow MAG {
         if (params.ancient_dna && !params.skip_ancient_damagecorrection) {
             BINNING(
                 BINNING_PREPARATION.out.grouped_mappings.join(ANCIENT_DNA_ASSEMBLY_VALIDATION.out.contigs_recalled).map { it -> [it[0], it[4], it[2], it[3]] },
-                ch_short_reads
+                ch_short_reads,
             )
         }
         else {
             BINNING(
                 BINNING_PREPARATION.out.grouped_mappings,
-                ch_short_reads
+                ch_short_reads,
             )
         }
         ch_versions = ch_versions.mix(BINNING.out.versions)
@@ -654,7 +657,7 @@ workflow MAG {
         }
         CAT(
             ch_input_for_postbinning,
-            ch_cat_db
+            ch_cat_db,
         )
         // Group all classification results for each sample in a single file
         ch_cat_summary = CAT.out.tax_classification_names.collectFile(keepHeader: true) { meta, classification ->
@@ -692,7 +695,7 @@ workflow MAG {
                     ch_gtdb_bins,
                     ch_bin_qc_summary,
                     gtdb,
-                    gtdb_mash
+                    gtdb_mash,
                 )
                 ch_versions = ch_versions.mix(GTDBTK.out.versions.first())
                 ch_gtdbtk_summary = GTDBTK.out.summary
@@ -709,7 +712,7 @@ workflow MAG {
                 ch_quast_bins_summary.ifEmpty([]),
                 ch_gtdbtk_summary.ifEmpty([]),
                 ch_cat_global_summary.ifEmpty([]),
-                params.binqc_tool
+                params.binqc_tool,
             )
         }
 
@@ -731,7 +734,7 @@ workflow MAG {
             PROKKA(
                 ch_bins_for_prokka,
                 [],
-                []
+                [],
             )
             ch_versions = ch_versions.mix(PROKKA.out.versions.first())
         }
@@ -758,9 +761,9 @@ workflow MAG {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_'  +  'mag_software_'  + 'mqc_'  + 'versions.yml',
+            name: 'nf_core_' + 'mag_software_' + 'mqc_' + 'versions.yml',
             sort: true,
-            newLine: true
+            newLine: true,
         )
         .set { ch_collated_versions }
 
@@ -798,7 +801,7 @@ workflow MAG {
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
             name: 'methods_description_mqc.yaml',
-            sort: true
+            sort: true,
         )
     )
 
@@ -832,7 +835,7 @@ workflow MAG {
         ch_multiqc_custom_config.toList(),
         ch_multiqc_logo.toList(),
         [],
-        []
+        [],
     )
 
     emit: