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Fix paired end sample handling #439

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Sep 25, 2024
Merged

Fix paired end sample handling #439

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7 changes: 4 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -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

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3 changes: 2 additions & 1 deletion conf/test_nextflex.config
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Expand Up @@ -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'
Expand All @@ -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

}

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1 change: 1 addition & 0 deletions subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
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Expand Up @@ -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 ]
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