From 3ff8de2a2670904f79f85e179e255dfec349f0d5 Mon Sep 17 00:00:00 2001
From: Adam Rosenbaum <adam.rosenbaum@regionvasterbotten.se>
Date: Fri, 29 Nov 2024 08:34:22 +0100
Subject: [PATCH] Fix longread hostremoval, and fix --longread_percentidentiy
 parameter in config

---
 conf/modules.config                        | 2 +-
 subworkflows/local/longread_hostremoval.nf | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index a1b3b1f4..90eca6f0 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -620,7 +620,7 @@ process {
     }
 
     withName: METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
-        ext.args = { meta.assembler in ['FLYE', 'METAMDBG'] ? "--percentIdentity ${params.longred_percentidentity}" : '' }
+        ext.args = { meta.assembler in ['FLYE', 'METAMDBG'] ? "--percentIdentity ${params.longread_percentidentity}" : '' }
         publishDir = [path: { "${params.outdir}/GenomeBinning/depths/contigs" }, mode: params.publish_dir_mode, pattern: '*-depth.txt.gz']
         ext.prefix = { "${meta.assembler}-${meta.id}-depth" }
     }
diff --git a/subworkflows/local/longread_hostremoval.nf b/subworkflows/local/longread_hostremoval.nf
index 4a43e7f7..a8c8bcd5 100644
--- a/subworkflows/local/longread_hostremoval.nf
+++ b/subworkflows/local/longread_hostremoval.nf
@@ -19,8 +19,9 @@ workflow LONGREAD_HOSTREMOVAL {
     ch_versions       = Channel.empty()
     ch_multiqc_files  = Channel.empty()
 
+    ch_host_reference = reference.map { [ [:], it ] }
 
-    ch_minimap2_index = MINIMAP2_HOST_INDEX ( [ [], reference ] ).index
+    ch_minimap2_index = MINIMAP2_HOST_INDEX ( ch_host_reference ).index
     ch_versions       = ch_versions.mix( MINIMAP2_HOST_INDEX.out.versions )
 
     MINIMAP2_HOST_ALIGN ( reads, ch_minimap2_index, true, 'bai', false, false )
@@ -45,7 +46,7 @@ workflow LONGREAD_HOSTREMOVAL {
     bam_bai = MINIMAP2_HOST_ALIGN.out.bam
         .join(SAMTOOLS_HOSTREMOVED_INDEX.out.bai)
 
-    SAMTOOLS_HOSTREMOVED_STATS ( bam_bai, [[],reference] )
+    SAMTOOLS_HOSTREMOVED_STATS ( bam_bai, ch_host_reference )
     ch_versions = ch_versions.mix(SAMTOOLS_HOSTREMOVED_STATS.out.versions.first())
     ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_HOSTREMOVED_STATS.out.stats )