Merge pull request #270 from nf-core/index-warn-fix

Fix broken check for host read removal index

CHANGELOG.md

@@ -9,6 +9,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files
+- [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
+
 ### `Dependencies`
 
 ### `Deprecated`

workflows/taxprofiler.nf

@@ -35,7 +35,8 @@ if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit
 if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' ))  exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"
 
 if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
-if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
+if (params.perform_shortread_hostremoval && !params.hostremoval_reference && params.shortread_hostremoval_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
+if (params.perform_longread_hostremoval && !params.hostremoval_reference && params.longread_hostremoval_index) { exit 1, "ERROR: [nf-core/taxprofiler] --longread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
 
 if (params.hostremoval_reference           ) { ch_reference = file(params.hostremoval_reference) }
 if (params.shortread_hostremoval_index     ) { ch_shortread_reference_index = Channel.fromPath(params.shortread_hostremoval_index).map{[[], it]} } else { ch_shortread_reference_index = [] }