Fix remainig failed merges

Author: jfy133

subworkflows/local/longread_hostremoval/main.nf

@@ -43,7 +43,8 @@ workflow LONGREAD_HOSTREMOVAL {
         // Join BAI back to BAM for host removal statistics
         bam_bai = MINIMAP2_ALIGN.out.bam.join(MINIMAP2_ALIGN.out.index)
 
-        ch_stats = SAMTOOLS_STATS(bam_bai, [[], ch_reference, []])
+        SAMTOOLS_STATS(bam_bai, [[], ch_reference, []])
+        ch_stats = SAMTOOLS_STATS.out.stats
         ch_multiqc_files = ch_multiqc_files.mix(SAMTOOLS_STATS.out.stats)
 
         // Generate unmapped reads FASTQ for downstream taxprofiling

subworkflows/local/shortread_hostremoval/main.nf

@@ -34,7 +34,7 @@ workflow SHORTREAD_HOSTREMOVAL {
 
     if (params.shortread_hostremoval_tool == 'bowtie2') {
         // Map, generate BAM with all reads and unmapped reads in FASTQ for downstream
-        BOWTIE2_ALIGN(reads, ch_hostremoval_index, [[], ch_reference], true, true)
+        BOWTIE2_ALIGN(ch_reads, ch_hostremoval_index, [[], ch_reference], true, true)
         ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions.first())
         ch_multiqc_files = ch_multiqc_files.mix(BOWTIE2_ALIGN.out.log)