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Merge pull request #79 from nf-core/fastp-complexity

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Add FASTP complexity option
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James A. Fellows Yates 2022-05-07 14:05:32 +02:00 committed by GitHub
commit fd71b71929
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10 changed files with 117 additions and 9 deletions
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2
.github/workflows/ci.yml vendored
View file

@ -38,7 +38,7 @@ jobs:
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq"
- "--shortread_complexityfilter_tool prinseqplusplus"
- "--perform_runmerging"
- "--perform_runmerging --shortread_clipmerge_mergepairs"
- "--shortread_complexityfilter false --perform_shortread_hostremoval"

6
conf/modules.config
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@ -54,7 +54,8 @@ process {
params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
// filtering options
"--length_required ${params.shortread_clipmerge_minlength}"
"--length_required ${params.shortread_clipmerge_minlength}",
(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
@ -74,7 +75,8 @@ process {
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
// filtering options
"--length_required ${params.shortread_clipmerge_minlength}"
"--length_required ${params.shortread_clipmerge_minlength}",
params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [

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
perform_runmerging = 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

46
conf/test_nopreprocessing.config Normal file
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@ -0,0 +1,46 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
----------------------------------------------------------------------------------------
*/
params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset skipping all preprocessing to check pipeline function'
// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
// Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_clipmerge = false
perform_longread_clip = false
perform_shortread_complexityfilter = false
perform_shortread_hostremoval = false
perform_longread_hostremoval = false
perform_runmerging = false
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
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
}
process {
withName: MALT_RUN {
maxForks = 1
}
}

46
conf/test_noprofiling.config Normal file
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@ -0,0 +1,46 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
----------------------------------------------------------------------------------------
*/
params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset without performing any profiling to check pipeline function'
// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'
// Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_clipmerge = true
perform_longread_clip = true
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
perform_longread_hostremoval = true
perform_runmerging = true
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
run_kaiju = false
run_kraken2 = false
run_malt = false
run_metaphlan3 = false
run_centrifuge = false
run_diamond = false
}
process {
withName: MALT_RUN {
maxForks = 1
}
}

6
docs/usage.md
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@ -183,11 +183,11 @@ Complexity filtering can be activated via the `--perform_shortread_complexityfil
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.
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/).
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).
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.
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 the tools (see links above) to decide on optimal methods and parameters for your dataset.
You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`.
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.
#### Host Removal

3
nextflow.config
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@ -74,6 +74,7 @@ params {
shortread_complexityfilter_bbduk_mask = false
shortread_complexityfilter_prinseqplusplus_mode = 'entropy'
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
shortread_complexityfilter_fastp_threshold = 30
save_complexityfiltered_reads = false
// run merging
@ -185,6 +186,8 @@ profiles {
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
}
// Load igenomes.config if required

7
nextflow_schema.json
View file

@ -319,7 +319,8 @@
},
"shortread_complexityfilter_tool": {
"type": "string",
"default": "bbduk"
"default": "bbduk",
"enum": ["bbduk", "prinseqplusplus", "fastp"]
},
"shortread_complexityfilter_bbduk_windowsize": {
"type": "integer",
@ -404,6 +405,10 @@
"longread_hostremoval_index": {
"type": "string",
"default": "None"
},
"shortread_complexityfilter_fastp_threshold": {
"type": "integer",
"default": 30
}
}
}

1
subworkflows/local/shortread_complexityfiltering.nf
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@ -13,6 +13,7 @@ workflow SHORTREAD_COMPLEXITYFILTERING {
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
ch_versions = ch_versions.mix( BBMAP_BBDUK.out.versions.first() )

8
workflows/taxprofiler.nf
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@ -19,9 +19,12 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
// Check mandatory parameters
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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.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'"
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." }
@ -131,7 +134,8 @@ workflow TAXPROFILER {
SUBWORKFLOW: COMPLEXITY FILTERING
*/
if ( params.perform_shortread_complexityfilter ) {
// fastp complexity filtering is activated via modules.conf in shortread_preprocessing
if ( params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp' ) {
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
} else {
@ -228,7 +232,7 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
}
if (params.perform_shortread_complexityfilter){
if (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp'){
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
}