fix(mqc): use active aligner display name for fail_mapped header

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1844](https://github.com/nf-core/rnaseq/pull/1844) - Bump version to 3.27.0dev after release 3.26.0; flip the MultiQC report links and RO-Crate URL/version back to dev
 - [PR #1848](https://github.com/nf-core/rnaseq/pull/1848) - Align `actions/checkout` SHA in `nf-test-arm.yml` and `nf-test-gpu.yml` with the template-derived `nf-test.yml` (`v6`) ([#1847](https://github.com/nf-core/rnaseq/issues/1847))
 - [PR #1849](https://github.com/nf-core/rnaseq/pull/1849) - Tidy-up batch addressing [#1845](https://github.com/nf-core/rnaseq/issues/1845): README/schema clarifications, `&` → `&&` in three guards, deduplicated `withName` blocks, and removal of the unmaintained `bin/fastq_dir_to_samplesheet.py` (use [nf-core/fetchngs](https://nf-co.re/fetchngs) for samplesheet generation)
+- [PR #1850](https://github.com/nf-core/rnaseq/pull/1850) - Use the active aligner's display name in the MultiQC `fail_mapped` per-sample status row, and drop the hardcoded "STAR" reference from the pipeline-completion `min_mapped_reads` warning, so Bowtie2 reports no longer mislabel the metric as STAR ([#1846](https://github.com/nf-core/rnaseq/issues/1846))
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07
 

subworkflows/local/multiqc_rnaseq/main.nf

@@ -18,6 +18,7 @@ workflow MULTIQC_RNASEQ {
     ch_strand_data             // channel: [ val(meta), provided, status, salmon, rseqc ] - per-sample strand classification, used for the Strandedness checks section
     ch_trim_read_count         // channel: [ val(meta), val(num_reads) ]   - for fail_trimmed section
     ch_percent_mapped_pass     // channel: [ id, percent_mapped, pass ]    - for fail_mapped section
+    aligner_display_name       // string: display name of the aligner used for the percent_mapped metric, e.g. 'STAR uniquely mapped reads' or 'Bowtie2 overall alignment rate'
     ch_fastq                   // channel: [ val(meta), [ reads ] ]
     ch_collated_versions       // channel: path(versions yaml)
     samplesheet_path           // path: pipeline input samplesheet
@@ -73,7 +74,7 @@ workflow MULTIQC_RNASEQ {
         .collectFile { id, percent_mapped, _pass ->
             [
                 "${id}_fail_mapped_samples_mqc.tsv",
-                sample_status_header.text + "Sample\tSTAR uniquely mapped reads (%)\n${id}\t${percent_mapped}\n",
+                sample_status_header.text + "Sample\t${aligner_display_name} (%)\n${id}\t${percent_mapped}\n",
             ]
         }
         .map { f -> [f.baseName.replace('_fail_mapped_samples_mqc', ''), f] }

subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf

@@ -878,7 +878,7 @@ def rnaseqSummary(monochrome_logs=true, pass_mapped_reads=[:], pass_trimmed_read
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_trimmed_count}/${pass_trimmed_reads.size()} samples skipped since they failed ${params.min_trimmed_reads} trimmed read threshold.${colors.reset}-"
         }
         if (fail_mapped_count > 0) {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_mapped_count}/${pass_mapped_reads.size()} samples skipped since they failed STAR ${params.min_mapped_reads}% mapped threshold.${colors.reset}-"
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_mapped_count}/${pass_mapped_reads.size()} samples skipped since they failed the ${params.min_mapped_reads}% mapped threshold.${colors.reset}-"
         }
         if (fail_strand_count > 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Please check MultiQC report: ${fail_strand_count}/${pass_strand_check.size()} samples failed strandedness check.${colors.reset}-"

workflows/rnaseq/main.nf

@@ -99,6 +99,15 @@ workflow RNASEQ {
     def ch_biotypes_header_multiqc   = file("$projectDir/workflows/rnaseq/assets/multiqc/biotypes_header.txt", checkIfExists: true)
     def ch_transcript_fasta_placeholder = ch_pca_header_multiqc
 
+    // Match the General Statistics column the active aligner emits so the
+    // MultiQC fail_mapped row reads consistently with the rest of the report.
+    def aligner_display_name = [
+        'star_salmon'    : 'STAR uniquely mapped reads',
+        'star_rsem'      : 'STAR uniquely mapped reads',
+        'hisat2'         : 'HISAT2 overall alignment rate',
+        'bowtie2_salmon' : 'Bowtie2 overall alignment rate',
+    ].get(params.aligner, 'Aligned reads')
+
     // Pre-build fasta_fai value channels for subworkflows that need [meta, fasta, fai]
     // .first() converts the queue channel to a value channel so it can be consumed multiple times
     ch_fasta_fai            = ch_fasta.combine(ch_fai).map { fasta, fai -> [ [:], fasta, fai ] }.first()
@@ -809,6 +818,7 @@ workflow RNASEQ {
             ch_strand_data,
             ch_trim_read_count,
             ch_genome_bam_bai_mapping.percent_mapped_pass,
+            aligner_display_name,
             ch_fastq,
             ch_collated_versions,
             params.input,