fix sample sheet tests with meta.id

CHANGELOG.md

@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `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`

workflows/ampliseq.nf

@@ -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)