mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:53:10 +00:00
Merge branch 'dev' into hostremoval
This commit is contained in:
commit
70f94603b0
10 changed files with 111 additions and 171 deletions
6
.github/workflows/ci.yml
vendored
6
.github/workflows/ci.yml
vendored
|
@ -29,8 +29,8 @@ jobs:
|
|||
- NXF_VER: ""
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NXF_EDGE: "1"
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parameters:
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- "--longread_clip false"
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- "--shortread_clip false"
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||||
- "--perform_longread_clip false"
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||||
- "--perform_shortread_clipmerge false"
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- "--shortread_clipmerge_tool fastp"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
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- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
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|
@ -39,6 +39,8 @@ jobs:
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- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseq"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_clipmerge_mergepairs"
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- "--shortread_complexityfilter false --shortread_hostremoval"
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steps:
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|
|
|
@ -179,9 +179,19 @@ process {
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]
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}
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withName: CAT_FASTQ {
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ext.prefix = { "${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/run_merging/" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_runmerged_reads
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]
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}
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/malt/${meta.db_name}" },
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mode: params.publish_dir_mode,
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|
@ -191,7 +201,7 @@ process {
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|||
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withName: KRAKEN2_KRAKEN2 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: params.publish_dir_mode,
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|
@ -200,12 +210,13 @@ process {
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}
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withName: METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/metaphlan3/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{biom,txt}'
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]
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ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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|
|
|
@ -22,16 +22,15 @@ params {
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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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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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shortread_clipmerge = true
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longread_clip = false
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shortread_complexityfilter = true
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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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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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perform_shortread_clipmerge = true
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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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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}
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|
|
|
@ -55,7 +55,7 @@ params {
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databases = null
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// FASTQ preprocessing
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shortread_clipmerge = false
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perform_shortread_clipmerge = false
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shortread_clipmerge_tool = 'fastp'
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shortread_clipmerge_skipadaptertrim = false
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shortread_clipmerge_mergepairs = false
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|
@ -63,11 +63,11 @@ params {
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|||
shortread_clipmerge_adapter1 = null
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shortread_clipmerge_adapter2 = null
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shortread_clipmerge_minlength = 15
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longread_clip = false
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perform_longread_clip = false
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save_preprocessed_reads = false
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||||
// Complexity filtering
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shortread_complexityfilter = false
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perform_shortread_complexityfilter = false
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shortread_complexityfilter_tool = 'bbduk'
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shortread_complexityfilter_entropy = 0.3
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shortread_complexityfilter_bbduk_windowsize = 50
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|
@ -76,6 +76,9 @@ params {
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|||
shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
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save_complexityfiltered_reads = false
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// run merging
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perform_runmerging = false
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save_runmerged_reads = false
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// Host Removal
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shortread_hostremoval = false
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|
@ -94,6 +97,7 @@ params {
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centrifuge_save_unaligned = false
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centrifuge_save_aligned = false
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centrifuge_sam_format = false
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// metaphlan3
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run_metaphlan3 = false
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}
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|
|
|
@ -262,15 +262,9 @@
|
|||
"type": "string",
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||||
"default": "None"
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||||
},
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||||
"shortread_clipmerge": {
|
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"type": "boolean"
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||||
},
|
||||
"shortread_clipmerge_excludeunmerged": {
|
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"type": "boolean"
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||||
},
|
||||
"longread_clip": {
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"type": "boolean"
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||||
},
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||||
"run_malt": {
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"type": "boolean"
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||||
},
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||||
|
@ -321,8 +315,7 @@
|
|||
"default": 15
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||||
},
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||||
"save_preprocessed_reads": {
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||||
"type": "boolean",
|
||||
"default": false
|
||||
"type": "boolean"
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||||
},
|
||||
"shortread_complexityfilter_tool": {
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"type": "string",
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||||
|
@ -335,9 +328,6 @@
|
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"shortread_complexityfilter_bbduk_mask": {
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||||
"type": "boolean"
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||||
},
|
||||
"shortread_complexityfilter": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"shortread_complexityfilter_entropy": {
|
||||
"type": "number",
|
||||
"default": 0.3
|
||||
|
@ -352,8 +342,22 @@
|
|||
"default": 0.5
|
||||
},
|
||||
"save_complexityfiltered_reads": {
|
||||
"type": "boolean",
|
||||
"default": false
|
||||
"type": "boolean"
|
||||
},
|
||||
"save_runmerged_reads": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"perform_shortread_clipmerge": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"perform_longread_clip": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"perform_shortread_complexityfilter": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"perform_runmerging": {
|
||||
"type": "boolean"
|
||||
},
|
||||
"shortread_hostremoval": {
|
||||
"type": "boolean"
|
||||
|
|
|
@ -1,61 +0,0 @@
|
|||
process CENTRIFUGE_CENTRIFUGE {
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tag "$meta.id"
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label 'process_high'
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||||
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||||
conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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||||
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
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||||
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
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||||
|
||||
input:
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||||
tuple val(meta), path(reads)
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path db
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val save_unaligned
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val save_aligned
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val sam_format
|
||||
|
||||
output:
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||||
tuple val(meta), path('*report.txt') , emit: report
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||||
tuple val(meta), path('*results.txt') , emit: results
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||||
tuple val(meta), path('*.sam') , optional: true, emit: sam
|
||||
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
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tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
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path "versions.yml" , emit: versions
|
||||
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||||
when:
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||||
task.ext.when == null || task.ext.when
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||||
|
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
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def unaligned = ''
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def aligned = ''
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if (meta.single_end) {
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unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
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aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
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||||
} else {
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unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
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aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
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||||
}
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||||
def sam_output = sam_format ? "--out-fmt 'sam'" : ''
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||||
"""
|
||||
## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
|
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db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
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centrifuge \\
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||||
-x \$db_name \\
|
||||
-p $task.cpus \\
|
||||
$paired \\
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--report-file ${prefix}.report.txt \\
|
||||
-S ${prefix}.results.txt \\
|
||||
$unaligned \\
|
||||
$aligned \\
|
||||
$sam_output \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
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END_VERSIONS
|
||||
"""
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||||
}
|
|
@ -1,66 +0,0 @@
|
|||
name: centrifuge_centrifuge
|
||||
description: Classifies metagenomic sequence data
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||||
keywords:
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- classify
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- metagenomics
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- fastq
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||||
- db
|
||||
tools:
|
||||
- centrifuge:
|
||||
description: Centrifuge is a classifier for metagenomic sequences.
|
||||
homepage: https://ccb.jhu.edu/software/centrifuge/
|
||||
documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
|
||||
doi: 10.1101/gr.210641.116
|
||||
licence: ["GPL v3"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- db:
|
||||
type: directory
|
||||
description: Path to directory containing centrifuge database files
|
||||
- save_unaligned:
|
||||
type: value
|
||||
description: If true unmapped fastq files are saved
|
||||
- save_aligned:
|
||||
type: value
|
||||
description: If true mapped fastq files are saved
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: |
|
||||
File containing a classification summary
|
||||
pattern: "*.{report.txt}"
|
||||
- results:
|
||||
type: file
|
||||
description: |
|
||||
File containing classification results
|
||||
pattern: "*.{results.txt}"
|
||||
- fastq_unmapped:
|
||||
type: file
|
||||
description: Unmapped fastq files
|
||||
pattern: "*.unmapped.fastq.gz"
|
||||
- fastq_mapped:
|
||||
type: file
|
||||
description: Mapped fastq files
|
||||
pattern: "*.mapped.fastq.gz"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@sofstam"
|
||||
- "@jfy133"
|
||||
- "@sateeshperi"
|
|
@ -9,8 +9,7 @@ include { METAPHLAN3 } from '../../modules/nf-core/modules/meta
|
|||
|
||||
workflow PROFILING {
|
||||
take:
|
||||
shortreads // [ [ meta ], [ reads ] ]
|
||||
longreads // [ [ meta ], [ reads ] ]
|
||||
reads // [ [ meta ], [ reads ] ]
|
||||
databases // [ [ meta ], path ]
|
||||
|
||||
main:
|
||||
|
@ -22,8 +21,14 @@ workflow PROFILING {
|
|||
*/
|
||||
|
||||
// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
|
||||
ch_input_for_profiling = shortreads
|
||||
.mix( longreads )
|
||||
ch_input_for_profiling = reads
|
||||
.map {
|
||||
meta, reads ->
|
||||
def meta_new = meta.clone()
|
||||
pairtype = meta_new['single_end'] ? '_se' : '_pe'
|
||||
meta_new['id'] = meta_new['id'] + pairtype
|
||||
[meta_new, reads]
|
||||
}
|
||||
.combine(databases)
|
||||
.branch {
|
||||
malt: it[2]['tool'] == 'malt'
|
||||
|
|
|
@ -28,8 +28,8 @@ workflow SHORTREAD_FASTP {
|
|||
.map {
|
||||
meta, reads ->
|
||||
def meta_new = meta.clone()
|
||||
meta_new['single_end'] = 1
|
||||
[ meta_new, reads ]
|
||||
meta_new['single_end'] = true
|
||||
[ meta_new, [ reads ].flatten() ]
|
||||
}
|
||||
|
||||
ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )
|
||||
|
|
|
@ -111,14 +111,14 @@ workflow TAXPROFILER {
|
|||
/*
|
||||
SUBWORKFLOW: PERFORM PREPROCESSING
|
||||
*/
|
||||
if ( params.shortread_clipmerge ) {
|
||||
if ( params.perform_shortread_clipmerge ) {
|
||||
|
||||
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
|
||||
} else {
|
||||
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
|
||||
}
|
||||
|
||||
if ( params.longread_clip ) {
|
||||
if ( params.perform_longread_clip ) {
|
||||
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
|
||||
.map { it -> [ it[0], [it[1]] ] }
|
||||
ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
|
||||
|
@ -130,7 +130,7 @@ workflow TAXPROFILER {
|
|||
SUBWORKFLOW: COMPLEXITY FILTERING
|
||||
*/
|
||||
|
||||
if ( params.shortread_complexityfilter ) {
|
||||
if ( params.perform_shortread_complexityfilter ) {
|
||||
ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
|
||||
} else {
|
||||
ch_shortreads_filtered = ch_shortreads_preprocessed
|
||||
|
@ -147,11 +147,48 @@ workflow TAXPROFILER {
|
|||
ch_shortreads_hostremoved = ch_shortreads_filtered
|
||||
}
|
||||
|
||||
*/
|
||||
|
||||
if ( params.perform_runmerging ) {
|
||||
|
||||
ch_reads_for_cat_branch = ch_shortreads_hostremoved
|
||||
.mix( ch_longreads_preprocessed )
|
||||
.map {
|
||||
meta, reads ->
|
||||
def meta_new = meta.clone()
|
||||
meta_new.remove('run_accession')
|
||||
[ meta_new, reads ]
|
||||
}
|
||||
.groupTuple()
|
||||
.map {
|
||||
meta, reads ->
|
||||
[ meta, reads.flatten() ]
|
||||
}
|
||||
.branch {
|
||||
meta, reads ->
|
||||
// we can't concatenate files if there is not a second run, we branch
|
||||
// here to separate them out, and mix back in after for efficiency
|
||||
cat: ( meta.single_end && reads.size() > 1 ) || ( !meta.single_end && reads.size() > 2 )
|
||||
skip: true
|
||||
}
|
||||
|
||||
ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
|
||||
.mix( ch_reads_for_cat_branch.skip )
|
||||
.map {
|
||||
meta, reads ->
|
||||
[ meta, [ reads ].flatten() ]
|
||||
}
|
||||
|
||||
} else {
|
||||
ch_reads_runmerged = ch_shortreads_hostremoved
|
||||
.mix( ch_longreads_preprocessed )
|
||||
}
|
||||
|
||||
/*
|
||||
SUBWORKFLOW: PROFILING
|
||||
*/
|
||||
|
||||
PROFILING ( ch_shortreads_hostremoved, ch_longreads_preprocessed, DB_CHECK.out.dbs )
|
||||
PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
|
||||
ch_versions = ch_versions.mix( PROFILING.out.versions )
|
||||
|
||||
/*
|
||||
|
@ -173,23 +210,28 @@ workflow TAXPROFILER {
|
|||
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
|
||||
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
|
||||
|
||||
if (params.shortread_clipmerge) {
|
||||
if (params.perform_shortread_clipmerge) {
|
||||
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
|
||||
}
|
||||
|
||||
if (params.longread_clip) {
|
||||
if (params.perform_longread_clip) {
|
||||
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
|
||||
}
|
||||
|
||||
if (params.shortread_complexityfilter){
|
||||
if (params.perform_shortread_complexityfilter){
|
||||
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
|
||||
ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
|
||||
}
|
||||
|
||||
if (params.shortread_hostremoval) {
|
||||
ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
|
||||
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
|
||||
}
|
||||
|
||||
if (params.perform_runmerging){
|
||||
ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
|
||||
}
|
||||
|
||||
ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc )
|
||||
|
|
Loading…
Reference in a new issue