From fbecfb6f3384d0c1c42c1333e2682ac174b37adb Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 17 Mar 2023 20:47:09 +0100 Subject: [PATCH] Fix broken check for host read removal index --- CHANGELOG.md | 3 +++ workflows/taxprofiler.nf | 3 ++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0bfa518..bd053cc 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index e44015f..25c8d76 100644 --- a/workflows/taxprofiler.nf +++ b/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 = [] }