millironx/taxprofiler
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Merge branch 'dev' into prototaxites-docs-updates

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Sofia Stamouli 2023-03-21 08:44:48 +01:00 committed by GitHub
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2
CHANGELOG.md
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@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Fixed` ### `Fixed`
- [#271](https://github.com/nf-core/taxprofiler/pull/271/files) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133) - [#271](https://github.com/nf-core/taxprofiler/pull/271/files) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
- [#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` ### `Dependencies`

3
workflows/taxprofiler.nf
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@ -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.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.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.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 = [] } if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = Channel.fromPath(params.shortread_hostremoval_index).map{[[], it]} } else { ch_shortread_reference_index = [] }