millironx/taxprofiler
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Change param to a more generic name

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ljmesi 2022-05-05 13:20:34 +02:00
parent 557d31dfd2
commit 6618e8cac6
5 changed files with 8 additions and 5 deletions
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1
conf/test.config
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@ -29,6 +29,7 @@ params {
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = true
run_kraken2 = true
run_malt = true

2
docs/usage.md
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@ -197,7 +197,7 @@ Similarly to complexity filtering, host-removal can be useful for runtime optimi
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.
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.
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.
> 💡 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.

1
nextflow.config
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@ -83,6 +83,7 @@ params {
// Host Removal
perform_shortread_hostremoval = false
perform_longread_hostremoval = false
hostremoval_reference = null
shortread_hostremoval_index = null
longread_hostremoval_index = null
save_hostremoval_index = false

1
nextflow_schema.json
View file

@ -365,6 +365,7 @@
"perform_longread_hostremoval": {
"type": "boolean"
},
"hostremoval_reference": {
"type": "string",
"default": "None"
},

8
workflows/taxprofiler.nf
View file

@ -11,7 +11,7 @@ WorkflowTaxprofiler.initialise(params, log)
// TODO nf-core: Add all file path parameters for the pipeline to the list below
// Check input path parameters to see if they exist
def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
def checkPathParamList = [ params.input, params.databases, params.hostremoval_reference,
params.shortread_hostremoval_index, params.multiqc_config
]
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
@ -22,10 +22,10 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
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."
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"
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." }
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." }
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.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
if (params.hostremoval_reference ) { ch_reference = file(params.hostremoval_reference) }
if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }