Merge pull request #439 from nschcolnicov/issue_415

Fix paired end sample handling

CHANGELOG.md

@@ -30,12 +30,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#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/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`.
-- [[#433]](https://github.com/nf-core/smrnaseq/pull/433) - Replace local instances of bowtie for nf-core [`bowtie2`](https://github.com/nf-core/smrnaseq/issues/434) and [`bowtie1`](https://github.com/nf-core/smrnaseq/issues/433) - Additionally adds a `bioawk` module that cleans fasta files.
+- [[#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
 - [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC and all modules to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC.
-- [[#435]](https://github.com/nf-core/smrnaseq/pull/435) - Update [Mirtop to latest version](https://github.com/nf-core/smrnaseq/issues/437) - Process samples separately and join results with `CSVTK_JOIN`.
+- [[#435]](https://github.com/nf-core/smrnaseq/pull/435) - Replace local instances of bowtie for nf-core [`bowtie2`](https://github.com/nf-core/smrnaseq/issues/434) and [`bowtie1`](https://github.com/nf-core/smrnaseq/issues/433) - Additionally adds a `bioawk` module that cleans fasta files.
+- [[#438]](https://github.com/nf-core/smrnaseq/pull/438) - Update [Mirtop to latest version](https://github.com/nf-core/smrnaseq/issues/437) - Process samples separately and join results with `CSVTK_JOIN`.
+- [[#439]](https://github.com/nf-core/smrnaseq/pull/439) - Fix [Fix paired end samples processing](https://github.com/nf-core/smrnaseq/issues/415) - Fix paired end sample handling and add test profile.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

conf/test_nextflex.config

@@ -9,7 +9,7 @@
 
 ----------------------------------------------------------------------------------------
 */
-// This test profile tests nextflex without genome
+// This test profile tests nextflex without genome and paired end sample handling
 
 params {
     config_profile_name        = 'Nextflex Test profile'
@@ -29,6 +29,7 @@ params {
 
     skip_mirdeep             = true
     save_intermediates       = true
+    //skip_fastp // this profile should not be used with skip_fastq to allow for testing paired end sample handling
 
 }
 

subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf

@@ -175,6 +175,7 @@ def validateInputSamplesheet(input) {
         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) }
+        metas[0].single_end = true
     }
 
     return [ metas[0], fastqs ]