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https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:53:10 +00:00
Add FASTP complexity option
This commit is contained in:
parent
e7b54801ed
commit
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9 changed files with 153 additions and 14 deletions
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@ -54,7 +54,8 @@ process {
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params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}"
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"--length_required ${params.shortread_clipmerge_minlength}",
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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@ -74,7 +75,8 @@ process {
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}"
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"--length_required ${params.shortread_clipmerge_minlength}",
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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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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perform_runmerging = 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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46
conf/test_nopreprocessing.config
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46
conf/test_nopreprocessing.config
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@ -0,0 +1,46 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset skipping all preprocessing to check pipeline function'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_clipmerge = false
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perform_longread_clip = false
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perform_shortread_complexityfilter = false
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perform_shortread_hostremoval = false
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perform_longread_hostremoval = false
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perform_runmerging = false
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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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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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}
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process {
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withName: MALT_RUN {
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maxForks = 1
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}
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}
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46
conf/test_noprofiling.config
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46
conf/test_noprofiling.config
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@ -0,0 +1,46 @@
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset without performing any profiling to check pipeline function'
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// Limit resources so that this can run on GitHub Actions
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max_cpus = 2
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max_memory = '6.GB'
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max_time = '6.h'
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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_clipmerge = true
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perform_longread_clip = true
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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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perform_runmerging = 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 = false
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run_kraken2 = false
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run_malt = false
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run_metaphlan3 = false
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run_centrifuge = false
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run_diamond = false
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}
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process {
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withName: MALT_RUN {
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maxForks = 1
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}
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}
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@ -183,11 +183,11 @@ Complexity filtering can be activated via the `--perform_shortread_complexityfil
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Complexity filtering is primarily a run-time optimisation step. It is not necessary for accurate taxonomic profiling, however it can speed up run-time of each tool by removing reads with low-diversity of nucleotides (e.g. with mono-nucleotide - `AAAAAAAA`, or di-nucleotide repeats `GAGAGAGAGAGAGAG`) that have a low-chance of giving an informative taxonomic ID as they can be associated with many different taxa. Removing these reads therefore saves computational time and resources.
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There are currently two options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) and [`prinseq++`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/).
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There are currently three options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/), [`prinseq++`](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus), and [`fastp`](https://github.com/OpenGene/fastp#low-complexity-filter).
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The tools offer different algorithms and parameters for removing low complexity reads. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of both tools (see links above) to decide on optimal methods and parameters for your dataset.
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You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`.
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You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`. If running with `fastp`, complexity filtering happens inclusively within the earlier shortread preprocessing step. Therefore there will not be an independent pipeline step for complexity filtering, and no independent FASTQ file (i.e. `--save_complexityfiltered_reads` will be ignored) - your complexity filtered reads will also be in the `fastp/` folder in the same file(s) as the preprocessed read.
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#### Host Removal
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@ -74,6 +74,7 @@ params {
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shortread_complexityfilter_bbduk_mask = false
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shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
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shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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shortread_complexityfilter_fastp_threshold = 30
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save_complexityfiltered_reads = false
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// run merging
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@ -185,6 +186,8 @@ profiles {
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}
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test { includeConfig 'conf/test.config' }
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test_full { includeConfig 'conf/test_full.config' }
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test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
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test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
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}
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// Load igenomes.config if required
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@ -10,7 +10,10 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -173,7 +176,14 @@
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"hidden": true
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},
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"email_on_fail": {
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@ -294,7 +304,10 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"]
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"enum": [
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"fastp",
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"adapterremoval"
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]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -319,7 +332,12 @@
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},
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk"
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"default": "bbduk",
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"enum": [
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"bbduk",
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"prinseqplusplus",
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"fastp"
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]
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},
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"shortread_complexityfilter_bbduk_windowsize": {
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"type": "integer",
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@ -335,7 +353,10 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"]
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"enum": [
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"entropy",
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"dust"
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]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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@ -391,7 +412,14 @@
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"kaiju_taxon_name": {
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"type": "string",
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"default": "species",
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"enum": ["phylum", "class", "order", "family", "genus", "species"]
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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]
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},
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"run_diamond": {
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"type": "boolean"
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@ -399,11 +427,19 @@
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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]
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},
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"longread_hostremoval_index": {
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"type": "string",
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"default": "None"
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}
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}
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}
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}
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@ -13,6 +13,7 @@ workflow SHORTREAD_COMPLEXITYFILTERING {
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
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if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
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ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
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ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() )
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@ -19,9 +19,12 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
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// Check mandatory parameters
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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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.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_clipmerge == false || params.shortread_clipmerge_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_clipmerge and/or --shortread_clipmerge_tool 'fastp'"
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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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@ -131,7 +134,8 @@ workflow TAXPROFILER {
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SUBWORKFLOW: COMPLEXITY FILTERING
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*/
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if ( params.perform_shortread_complexityfilter ) {
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// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
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if ( params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp' ) {
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ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
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ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
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} else {
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@ -228,7 +232,7 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
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}
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if (params.perform_shortread_complexityfilter){
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if (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp'){
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
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}
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