Pass --skip-dup-check to RustQC when --with_umi is set

UMI deduplication (UMICollapse / UMI-tools) physically removes PCR
duplicates, so the BAM has no reads flagged 0x400. RustQC's
duplicate-marking preflight check then aborts --use_rustqc --with_umi
runs. Duplication QC is not applicable to a deduplicated BAM, so pass
--skip-dup-check in the UMI path. The --use_rustqc + --skip_markduplicates
combination remains blocked in validateInputParameters() (there
duplicates are present-but-unmarked, so bypassing would be incorrect).

Closes #1881

Author: FelixKrueger

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1862](https://github.com/nf-core/rnaseq/pull/1862) - Correct the `docs/usage.md` note to state that `--extra_star_align_args` applies to `--aligner star_rsem`, since STAR runs as a standalone step and RSEM quantifies the resulting BAM ([#1857](https://github.com/nf-core/rnaseq/issues/1857))
 - [PR #1864](https://github.com/nf-core/rnaseq/pull/1864) - Bump nf-schema to 2.7.2, fixing boolean CLI parameter validation failures under Nextflow 26.x strict syntax ([#1860](https://github.com/nf-core/rnaseq/issues/1860))
 - [PR #1869](https://github.com/nf-core/rnaseq/pull/1869) - Add pipeline validation error when `--use_rustqc` and `--skip_markduplicates` are set together, since RustQC requires duplicate-marked BAM files ([#1865](https://github.com/nf-core/rnaseq/issues/1865))
+- [PR #1882](https://github.com/nf-core/rnaseq/pull/1882) - Pass `--skip-dup-check` to RustQC when `--with_umi` is set, so `--use_rustqc` works with UMI-deduplicated BAMs: UMICollapse / UMI-tools physically remove PCR duplicates, leaving no reads flagged `0x400`, so duplication QC is not applicable and RustQC's duplicate-marking check would otherwise abort the run ([#1881](https://github.com/nf-core/rnaseq/issues/1881))
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07
 

conf/modules/rustqc.config

@@ -8,6 +8,12 @@ process {
                 biotype_attr ? "--biotype-attribute ${biotype_attr}" : '',
                 '--preseq-seed 1 --preseq-seg-len 100000000',
                 '--tin-seed 1 --junction-saturation-seed 1',
+                // UMI dedup (UMICollapse / UMI-tools) physically removes PCR duplicates, so the
+                // BAM has no reads flagged 0x400 and duplication QC does not apply; bypass RustQC's
+                // duplicate-marking check. The --use_rustqc + --skip_markduplicates combination is
+                // instead blocked in validateInputParameters(), because there duplicates are
+                // present-but-unmarked and bypassing would produce incorrect duplication metrics.
+                params.with_umi ? '--skip-dup-check' : '',
             ].join(' ').trim()
         }
         publishDir = [

tests/rustqc.nf.test

@@ -46,6 +46,57 @@ nextflow_pipeline {
         }
     }
 
+    test("Params: use_rustqc --with_umi") {
+
+        when {
+            params {
+                outdir                  = "$outputDir"
+                use_rustqc              = true
+                with_umi                = true
+                umitools_extract_method = "regex"
+                umitools_bc_pattern     = "^(?P<umi_1>CGA.{8}){s<=2}.*"
+                umi_dedup_tool          = 'umicollapse'
+                skip_bbsplit            = true
+                // UMI dedup removes PCR duplicates, so RustQC runs with --skip-dup-check;
+                // this guards that --use_rustqc --with_umi completes instead of aborting.
+                skip_stringtie          = true
+                skip_bigwig             = true
+                skip_pseudo_alignment   = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore_rustqc')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
+                    removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+
+        cleanup {
+            // Only prune/delete on CI - keeping local VM state intact prevents
+            // cross-test launchDir wipes that break nf-test snapshot walks.
+            if (System.getenv("CI") == "true") {
+                if (System.getenv("NFT_PROFILE")?.contains("docker")) {
+                    "docker system prune -a -f --volumes".execute()
+                }
+                new File("${launchDir}").deleteDir()
+            }
+        }
+    }
+
     test("Params: use_rustqc - stub") {
 
         options "-stub"