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Add parameter for turning on longread host removal
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4 changed files with 6 additions and 4 deletions
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@ -28,7 +28,7 @@ params {
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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perform_longread_hostremoval = true
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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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@ -191,7 +191,7 @@ You can optionally save the FASTQ output of the run merging with the `--save_com
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#### Host Removal
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Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval`
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Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval` or `--perform_longread_hostremoval`.
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Similarly to complexity filtering, host-removal can be useful for runtime optimisation and reduction in misclassified reads. It is not always necessary to report classification of reads from a host when you already know the host of the sample, therefore you can gain a run-time and computational advantage by removing these prior typically resource-heavy profiling with more efficient methods. Furthermore, particularly with human samples, you can reduce the number of false positives during profiling that occur due to host-sequence contamination in reference genomes on public databases.
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@ -82,7 +82,7 @@ params {
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// Host Removal
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perform_shortread_hostremoval = false
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shortread_hostremoval_reference = null
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perform_longread_hostremoval = false
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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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@ -362,7 +362,9 @@
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"perform_shortread_hostremoval": {
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"type": "boolean"
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},
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"shortread_hostremoval_reference": {
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"perform_longread_hostremoval": {
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"type": "boolean"
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},
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"type": "string",
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"default": "None"
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},
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