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fix sample sheet tests with meta.id #761

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Jul 15, 2024
Merged

fix sample sheet tests with meta.id #761

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71cfa79
fix sample sheet tests with meta.id
d4straub Jul 15, 2024
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d4straub Jul 15, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#761](https://github.com/nf-core/ampliseq/pull/761) - Some sample sheet checks were not applied due to changes in the metadata ["meta"] structure in version 2.9.0

### `Dependencies`

### `Removed`
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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 isn't 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 aren't 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 aren't 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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