mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 06:53:10 +00:00
Added database preparation and final channel for profiling
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parent
cf55cc592c
commit
278f5605ca
6 changed files with 161 additions and 47 deletions
25
modules/local/database_check.nf
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25
modules/local/database_check.nf
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@ -0,0 +1,25 @@
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process DATABASE_CHECK {
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tag "$databasesheet"
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conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/python:3.8.3' :
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'quay.io/biocontainers/python:3.8.3' }"
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input:
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path databasesheet
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output:
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path '*.csv' , emit: csv
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path "versions.yml", emit: versions
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script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
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"""
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cat $databasesheet >> database_sheet.valid.csv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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python: \$(python --version | sed 's/Python //g')
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END_VERSIONS
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"""
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}
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@ -50,6 +50,9 @@ params {
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max_cpus = 16
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max_time = '240.h'
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// Databaess
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databases = null
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// FASTQ preprocessing
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fastp_clip_merge = false
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fastp_exclude_unmerged = true
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40
subworkflows/local/db_check.nf
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40
subworkflows/local/db_check.nf
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@ -0,0 +1,40 @@
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//
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// Check input samplesheet and get read channels
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//
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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workflow DB_CHECK {
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take:
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dbsheet // file: /path/to/dbsheet.csv
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main:
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// TODO: make database sheet check
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parsed_samplesheet = DATABASE_CHECK ( dbsheet )
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.csv
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.splitCsv ( header:true, sep:',' )
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.dump(tag: "db_split_csv_out")
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.map { create_db_channels(it) }
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.dump(tag: "db_channel_prepped")
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.set{ dbs }
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emit:
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dbs // channel: [ val(meta), [ db ] ]
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versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ]
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}
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def create_db_channels(LinkedHashMap row) {
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def meta = [:]
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meta.tool = row.tool
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meta.db_name = row.db_name
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meta.db_params = row.db_params
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def array = []
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if (!file(row.db_path, type: 'dir').exists()) {
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exit 1, "ERROR: Please check input samplesheet -> database could not be found!\n${row.db_path}"
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}
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array = [ meta, file(row.db_path) ]
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return array
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}
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@ -12,7 +12,7 @@ workflow INPUT_CHECK {
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parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
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.csv
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.splitCsv ( header:true, sep:',' )
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.dump(tag: "split_csv_out")
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.dump(tag: "input_split_csv_out")
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.branch {
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fasta: it['fasta'] != ''
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fastq: true
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73
subworkflows/local/preprocessing.nf
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73
subworkflows/local/preprocessing.nf
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@ -0,0 +1,73 @@
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//
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// Check input samplesheet and get read channels
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//
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include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
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include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
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workflow FASTQ_PREPROCESSING {
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take:
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reads // file: /path/to/samplesheet.csv
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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//
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// STEP: Read clipping and merging
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//
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// TODO give option to clip only and retain pairs
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// TODO give option to retain singletons (probably fastp option likely)
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// TODO move to subworkflow
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if ( params.fastp_clip_merge ) {
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ch_input_for_fastp = reads
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.dump(tag: "pre-fastp_branch")
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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}
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ch_input_for_fastp.single.dump(tag: "input_fastp_single")
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ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
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FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
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FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
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ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
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.mix( FASTP_SINGLE.out.reads )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = 1
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[ meta_new, reads ]
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}
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FASTQC_POST ( ch_fastp_reads_prepped )
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ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
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ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
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ch_processed_reads = ch_fastp_reads_prepped
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ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
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ch_multiqc_files.dump(tag: "preprocessing_mqc_final")
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} else {
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ch_processed_reads = reads
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}
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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@ -11,11 +11,12 @@ WorkflowTaxprofiler.initialise(params, log)
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// TODO nf-core: Add all file path parameters for the pipeline to the list below
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// Check input path parameters to see if they exist
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def checkPathParamList = [ params.input, params.multiqc_config ]
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def checkPathParamList = [ params.input, params.databases, params.multiqc_config ]
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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.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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/*
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========================================================================================
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@ -35,7 +36,11 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
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//
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// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
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//
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include { INPUT_CHECK } from '../subworkflows/local/input_check'
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include { INPUT_CHECK } from '../subworkflows/local/input_check'
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include { DB_CHECK } from '../subworkflows/local/db_check'
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include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing'
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/*
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========================================================================================
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@ -50,9 +55,6 @@ include { FASTQC } from '../modules/nf-core/modules/fastqc/
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include { MULTIQC } from '../modules/nf-core/modules/multiqc/main'
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include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
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include { FASTP as FASTP_SINGLE } from '../modules/nf-core/modules/fastp/main'
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include { FASTP as FASTP_PAIRED } from '../modules/nf-core/modules/fastp/main'
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include { FASTQC as FASTQC_POST } from '../modules/nf-core/modules/fastqc/main'
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include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
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/*
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)
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ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
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DB_CHECK (
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ch_databases
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)
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//
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// MODULE: Run FastQC
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//
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//
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// MODULE: Run Clip/Merge/Complexity
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//
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// TODO give option to clip only and retain pairs
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// TODO give option to retain singletons (probably fastp option likely)
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// TODO move to subworkflow
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if ( params.fastp_clip_merge ) {
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ch_input_for_fastp = INPUT_CHECK.out.fastq
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.dump(tag: "pre-fastp_branch")
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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}
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ch_input_for_fastp.single.dump(tag: "input_fastp_single")
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ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
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FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
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FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
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ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
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.mix( FASTP_SINGLE.out.reads )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = 1
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[ meta_new, reads ]
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}
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FASTQC_POST ( ch_fastp_reads_prepped )
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ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
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ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
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ch_processed_reads = ch_fastp_reads_prepped
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} else {
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ch_processed_reads = INPUT_CHECK.out.fastq
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FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq )
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}
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// MODULE: Cat merge runs of same sample
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ch_processed_for_combine = ch_processed_reads
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ch_processed_for_combine = FASTQ_PREPROCESSING.out.reads
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.dump(tag: "prep_for_combine_grouping")
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.map {
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meta, reads ->
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@ -153,6 +124,10 @@ workflow TAXPROFILER {
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.mix( CAT_FASTQ.out.reads )
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.dump(tag: "files_for_profiling")
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// Combine reads with possible databases
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ch_reads_for_profiling.combine(DB_CHECK.out.dbs).dump(tag: "reads_plus_db")
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//
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// MODULE: MultiQC
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//
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ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
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if (params.fastp_clip_merge) {
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ch_multiqc_files = ch_multiqc_files.mix(FASTP_SINGLE.out.json.collect{it[1]}.ifEmpty([]))
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ch_multiqc_files = ch_multiqc_files.mix(FASTP_PAIRED.out.json.collect{it[1]}.ifEmpty([]))
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ch_multiqc_files = ch_multiqc_files.mix(FASTQC_POST.out.zip.collect{it[1]}.ifEmpty([]))
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ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc)
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}
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