Merge pull request #430 from atrigila/pe_warning

Emit a warning upon supply of PE data

CHANGELOG.md

@@ -29,7 +29,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#405]](https://github.com/nf-core/smrnaseq/pull/405) - Fix [Umicollapse algo wrong set](https://github.com/nf-core/smrnaseq/issues/404) - Fix potential bug in Umicollapse (not effective as we do not allow PE data in smrnaseq - but for consistency)
 - [[#420]](https://github.com/nf-core/smrnaseq/pull/420) - Fix [mirTrace produces an error in test nextflex](https://github.com/nf-core/smrnaseq/issues/419) - Allow config mode to be used in mirtrace/qc
 - [[#425]](https://github.com/nf-core/smrnaseq/pull/425) - Raise [minimum required NXF version for pipeline](https://github.com/nf-core/smrnaseq/issues/424) - usage of `arity` in some modules now requires this
-- [[#426]](https://github.com/nf-core/smrnaseq/pull/426) - Add [nf-core mirtop](https://github.com/nf-core/smrnaseq/issues/417) - replace local `mirtop`
+- [[#426]](https://github.com/nf-core/smrnaseq/pull/426) - Add [nf-core mirtop](https://github.com/nf-core/smrnaseq/issues/426) - replace local for nf-core `mirtop`
+- [[#430]](https://github.com/nf-core/smrnaseq/pull/430) - Emit a [warning if paired-end end data is used](https://github.com/nf-core/smrnaseq/issues/423) - pipeline handles SE data
 - [[#427]](https://github.com/nf-core/smrnaseq/pull/427) - Add [nf-core pigz uncompress](https://github.com/nf-core/smrnaseq/issues/422) - replace local `mirdeep_pigz`
 - [[#429]](https://github.com/nf-core/smrnaseq/pull/429) - Make [saving of intermediate files optional](https://github.com/nf-core/smrnaseq/issues/424) - Allows user to choose whether to save intermediate files or not. Replaces several params that referred to the same such as `params.save_aligned` and `params.save_aligned_mirna_quant`.
 

subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf

@@ -170,6 +170,13 @@ def validateInputSamplesheet(input) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
 
+    // Emit a warning if `single_end` is false
+    if (metas[0].single_end == false) {
+        log.warn "Sample ${metas[0].id} is detected as paired-end reads (fastq_1 and fastq_2). The pipeline only handles SE data. Samplesheets with fastq_1 and fastq_2 are supported but fastq_2 is removed."
+        // Remove fastq_2 from the list and keep only fastq_1
+        fastqs = fastqs.collect { it.take(1) }
+    }
+
     return [ metas[0], fastqs ]
 }
 //