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Change param to a more generic name
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5 changed files with 8 additions and 5 deletions
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@ -29,6 +29,7 @@ params {
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = true
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run_kraken2 = true
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run_malt = true
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@ -197,7 +197,7 @@ Similarly to complexity filtering, host-removal can be useful for runtime optimi
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nf-core/taxprofiler currently offers host-removal via alignment against a reference genome with Bowtie2, and the use of the unaligned reads for downstream profiling.
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You can supply your reference genome in FASTA format with `--shortread_hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used.
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You can supply your reference genome in FASTA format with `--hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used.
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> 💡 If you have multiple taxa or sequences you wish to remove (e.g., the host genome and then also PhiX - common quality-control reagent during sequencing) you can simply concatenate the FASTAs of each taxa or sequences into a single reference file.
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@ -83,6 +83,7 @@ params {
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// Host Removal
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perform_shortread_hostremoval = false
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perform_longread_hostremoval = false
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hostremoval_reference = null
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shortread_hostremoval_index = null
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longread_hostremoval_index = null
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save_hostremoval_index = false
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@ -365,6 +365,7 @@
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"perform_longread_hostremoval": {
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"type": "boolean"
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},
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"hostremoval_reference": {
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"type": "string",
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"default": "None"
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},
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@ -11,7 +11,7 @@ WorkflowTaxprofiler.initialise(params, log)
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// TODO nf-core: Add all file path parameters for the pipeline to the list below
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// Check input path parameters to see if they exist
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def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
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def checkPathParamList = [ params.input, params.databases, params.hostremoval_reference,
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params.shortread_hostremoval_index, params.multiqc_config
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]
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for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
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@ -22,10 +22,10 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
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if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
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if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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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." }
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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." }
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
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if (params.hostremoval_reference ) { ch_reference = file(params.hostremoval_reference) }
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if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
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if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
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