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Added database preparation and final channel for profiling

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This commit is contained in:
James Fellows Yates 2022-02-19 12:36:08 +01:00
parent cf55cc592c
commit 278f5605ca
6 changed files with 161 additions and 47 deletions
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25
modules/local/database_check.nf Normal file
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@ -0,0 +1,25 @@
process DATABASE_CHECK {
tag "$databasesheet"
conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
'quay.io/biocontainers/python:3.8.3' }"
input:
path databasesheet
output:
path '*.csv' , emit: csv
path "versions.yml", emit: versions
script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
"""
cat $databasesheet >> database_sheet.valid.csv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
}

3
nextflow.config
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@ -50,6 +50,9 @@ params {
max_cpus = 16
max_time = '240.h'
// Databaess
databases = null
// FASTQ preprocessing
fastp_clip_merge = false
fastp_exclude_unmerged = true

40
subworkflows/local/db_check.nf Normal file
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@ -0,0 +1,40 @@
//
// Check input samplesheet and get read channels
//
include { DATABASE_CHECK } from '../../modules/local/database_check'
workflow DB_CHECK {
take:
dbsheet // file: /path/to/dbsheet.csv
main:
// TODO: make database sheet check
parsed_samplesheet = DATABASE_CHECK ( dbsheet )
.csv
.splitCsv ( header:true, sep:',' )
.dump(tag: "db_split_csv_out")
.map { create_db_channels(it) }
.dump(tag: "db_channel_prepped")
.set{ dbs }
emit:
dbs // channel: [ val(meta), [ db ] ]
versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ]
}
def create_db_channels(LinkedHashMap row) {
def meta = [:]
meta.tool = row.tool
meta.db_name = row.db_name
meta.db_params = row.db_params
def array = []
if (!file(row.db_path, type: 'dir').exists()) {
exit 1, "ERROR: Please check input samplesheet -> database could not be found!\n${row.db_path}"
}
array = [ meta, file(row.db_path) ]
return array
}

2
subworkflows/local/input_check.nf
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@ -12,7 +12,7 @@ workflow INPUT_CHECK {
parsed_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
.csv
.splitCsv ( header:true, sep:',' )
.dump(tag: "split_csv_out")
.dump(tag: "input_split_csv_out")
.branch {
fasta: it['fasta'] != ''
fastq: true

73
subworkflows/local/preprocessing.nf Normal file
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@ -0,0 +1,73 @@
//
// Check input samplesheet and get read channels
//
include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main'
include { FASTQC as FASTQC_POST } from '../../modules/nf-core/modules/fastqc/main'
workflow FASTQ_PREPROCESSING {
take:
reads // file: /path/to/samplesheet.csv
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
//
// STEP: Read clipping and merging
//
// TODO give option to clip only and retain pairs
// TODO give option to retain singletons (probably fastp option likely)
// TODO move to subworkflow
if ( params.fastp_clip_merge ) {
ch_input_for_fastp = reads
.dump(tag: "pre-fastp_branch")
.branch{
single: it[0]['single_end'] == true
paired: it[0]['single_end'] == false
}
ch_input_for_fastp.single.dump(tag: "input_fastp_single")
ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
.mix( FASTP_SINGLE.out.reads )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
FASTQC_POST ( ch_fastp_reads_prepped )
ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
ch_processed_reads = ch_fastp_reads_prepped
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_POST.out.zip.collect{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
ch_multiqc_files.dump(tag: "preprocessing_mqc_final")
} else {
ch_processed_reads = reads
}
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
mqc = ch_multiqc_files
}

63
workflows/taxprofiler.nf
View file

@ -11,11 +11,12 @@ WorkflowTaxprofiler.initialise(params, log)
// TODO nf-core: Add all file path parameters for the pipeline to the list below
// Check input path parameters to see if they exist
def checkPathParamList = [ params.input, params.multiqc_config ]
def checkPathParamList = [ params.input, params.databases, params.multiqc_config ]
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.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!' }
/*
========================================================================================
@ -37,6 +38,10 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
//
include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { DB_CHECK } from '../subworkflows/local/db_check'
include { FASTQ_PREPROCESSING } from '../subworkflows/local/preprocessing'
/*
========================================================================================
IMPORT NF-CORE MODULES/SUBWORKFLOWS
@ -50,9 +55,6 @@ include { FASTQC } from '../modules/nf-core/modules/fastqc/
include { MULTIQC } from '../modules/nf-core/modules/multiqc/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
include { FASTP as FASTP_SINGLE } from '../modules/nf-core/modules/fastp/main'
include { FASTP as FASTP_PAIRED } from '../modules/nf-core/modules/fastp/main'
include { FASTQC as FASTQC_POST } from '../modules/nf-core/modules/fastqc/main'
include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
/*
@ -76,6 +78,10 @@ workflow TAXPROFILER {
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
DB_CHECK (
ch_databases
)
//
// MODULE: Run FastQC
//
@ -91,47 +97,12 @@ workflow TAXPROFILER {
//
// MODULE: Run Clip/Merge/Complexity
//
// TODO give option to clip only and retain pairs
// TODO give option to retain singletons (probably fastp option likely)
// TODO move to subworkflow
if ( params.fastp_clip_merge ) {
ch_input_for_fastp = INPUT_CHECK.out.fastq
.dump(tag: "pre-fastp_branch")
.branch{
single: it[0]['single_end'] == true
paired: it[0]['single_end'] == false
FASTQ_PREPROCESSING ( INPUT_CHECK.out.fastq )
}
ch_input_for_fastp.single.dump(tag: "input_fastp_single")
ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
FASTP_PAIRED ( ch_input_for_fastp.paired, false, true )
ch_fastp_reads_prepped = FASTP_PAIRED.out.reads_merged
.mix( FASTP_SINGLE.out.reads )
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
FASTQC_POST ( ch_fastp_reads_prepped )
ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
ch_processed_reads = ch_fastp_reads_prepped
} else {
ch_processed_reads = INPUT_CHECK.out.fastq
}
// MODULE: Cat merge runs of same sample
ch_processed_for_combine = ch_processed_reads
ch_processed_for_combine = FASTQ_PREPROCESSING.out.reads
.dump(tag: "prep_for_combine_grouping")
.map {
meta, reads ->
@ -153,6 +124,10 @@ workflow TAXPROFILER {
.mix( CAT_FASTQ.out.reads )
.dump(tag: "files_for_profiling")
// Combine reads with possible databases
ch_reads_for_profiling.combine(DB_CHECK.out.dbs).dump(tag: "reads_plus_db")
//
// MODULE: MultiQC
//
@ -166,9 +141,7 @@ 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.fastp_clip_merge) {
ch_multiqc_files = ch_multiqc_files.mix(FASTP_SINGLE.out.json.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FASTP_PAIRED.out.json.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FASTQC_POST.out.zip.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(FASTQ_PREPROCESSING.out.mqc)
}