Fix rnaseq preprocessing: don't trim with bad linting (#7881)

pinin4fjords · web-flow · commit 826975544c32 · 2025-03-21T15:07:07.000Z
diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
@@ -153,7 +153,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
         )
         ch_versions = ch_versions.mix(FQ_LINT.out.versions.first())
         ch_lint_log = ch_lint_log.mix(FQ_LINT.out.lint)
-        ch_reads = ch_reads.join(FQ_LINT.out.lint.map{it[0]})
+        ch_filtered_reads = ch_reads.join(FQ_LINT.out.lint.map{it[0]})
     }
 
     //

Original file line number	Diff line number	Diff line change
`@@ -153,7 +153,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {`
`153`	`153`	`)`
`154`	`154`	`ch_versions = ch_versions.mix(FQ_LINT.out.versions.first())`
`155`	`155`	`ch_lint_log = ch_lint_log.mix(FQ_LINT.out.lint)`
`156`		`- ch_reads = ch_reads.join(FQ_LINT.out.lint.map{it[0]})`
	`156`	`+ ch_filtered_reads = ch_reads.join(FQ_LINT.out.lint.map{it[0]})`
`157`	`157`	`}`
`158`	`158`
`159`	`159`	`//`