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Fix meta.id to meta.sample for early tests on sample sheet #760

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Fix meta.id to meta.sample for early tests on sample sheet #760

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232ac58
bump version to 2.11.0dev
d4straub Jul 15, 2024
48ee1b9
fix sample sheet tests with meta.id
d4straub Jul 15, 2024
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14 changes: 14 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,20 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## nf-core/ampliseq version 2.11.0dev

### `Added`

### `Changed`

### `Fixed`

- [#760](https://github.com/nf-core/ampliseq/pull/760) - Some sample sheet checks were not applied due to changes in the metadata ["meta"] structure in version 2.9.0

### `Dependencies`

### `Removed`

## nf-core/ampliseq version 2.10.0 - 2024-06-27

### `Added`
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/ampliseq/releases/tag/2.10.0" target="_blank">nf-core/ampliseq</a>
This report has been generated by the <a href="https://github.com/nf-core/ampliseq/tree/dev" target="_blank">nf-core/ampliseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/ampliseq/2.10.0/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/ampliseq/dev/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-ampliseq-methods-description":
order: -1000
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -356,7 +356,7 @@ manifest {
description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '2.10.0'
version = '2.11.0dev'
doi = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420'
}

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8 changes: 4 additions & 4 deletions workflows/ampliseq.nf
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Expand Up @@ -268,13 +268,13 @@ workflow AMPLISEQ {
ch_input_reads = Channel.empty()
if ( params.input ) {
// See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
ch_input_reads = Channel.fromSamplesheet("input")
ch_input_reads = Channel.fromSamplesheet("input") // meta: meta.sample, meta.run
.map{ meta, readfw, readrv ->
meta.single_end = single_end.toBoolean()
def reads = single_end ? readfw : [readfw,readrv]
if ( !meta.single_end && !readrv ) { error("Entry `reverseReads` is missing in $params.input for $meta.id, either correct the samplesheet or use `--single_end`, `--pacbio`, or `--iontorrent`") } // make sure that reverse reads are present when single_end isnt specified
if ( !meta.single_end && ( readfw.getSimpleName() == meta.id || readrv.getSimpleName() == meta.id ) ) { error("Entry `sampleID` cannot be identical to simple name of `forwardReads` or `reverseReads`, please change `sampleID` in $params.input for sample $meta.id") } // sample name and any file name without extensions arent identical, because rename_raw_data_files.nf would forward 3 files (2 renamed +1 input) instead of 2 in that case
if ( meta.single_end && ( readfw.getSimpleName() == meta.id+"_1" || readfw.getSimpleName() == meta.id+"_2" ) ) { error("Entry `sampleID`+ `_1` or `_2` cannot be identical to simple name of `forwardReads`, please change `sampleID` in $params.input for sample $meta.id") } // sample name and file name without extensions arent identical, because rename_raw_data_files.nf would forward 2 files (1 renamed +1 input) instead of 1 in that case
if ( !meta.single_end && !readrv ) { error("Entry `reverseReads` is missing in $params.input for $meta.sample, either correct the samplesheet or use `--single_end`, `--pacbio`, or `--iontorrent`") } // make sure that reverse reads are present when single_end isnt specified
if ( !meta.single_end && ( readfw.getSimpleName() == meta.sample || readrv.getSimpleName() == meta.sample ) ) { error("Entry `sampleID` cannot be identical to simple name of `forwardReads` or `reverseReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and any file name without extensions arent identical, because rename_raw_data_files.nf would forward 3 files (2 renamed +1 input) instead of 2 in that case
if ( meta.single_end && ( readfw.getSimpleName() == meta.sample+"_1" || readfw.getSimpleName() == meta.sample+"_2" ) ) { error("Entry `sampleID`+ `_1` or `_2` cannot be identical to simple name of `forwardReads`, please change `sampleID` in $params.input for sample $meta.sample") } // sample name and file name without extensions arent identical, because rename_raw_data_files.nf would forward 2 files (1 renamed +1 input) instead of 1 in that case
return [meta, reads] }
} else if ( params.input_fasta ) {
ch_input_fasta = Channel.fromPath(params.input_fasta, checkIfExists: true)
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