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Merge pull request #10 from muneebdev7/dev
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Merging dev into master
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@muneebdev7
muneebdev7 authored Nov 24, 2024
2 parents b2d4da3 + c6fd7bf commit 420dddd
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Showing 2 changed files with 164 additions and 9 deletions.
109 changes: 104 additions & 5 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -19,15 +19,114 @@ process {
]

withName: FASTQC {
ext.args = '--quiet'
ext.args = '--quiet'
publishDir = [
path: { "${params.outdir}/fastqc" },
mode: params.publish_dir_mode,
pattern: "*.html"
]
ext.prefix = { "${meta.id}_raw" }
tag = { "${meta.id}_raw" }
}
withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }

withName: FASTP {
ext.args = [
"-q ${params.fastp_qualified_quality}",
"--cut_front",
"--cut_tail",
"--cut_mean_quality ${params.fastp_cut_mean_quality}",
"--length_required ${params.reads_minlength}"
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/multiqc" },
[
path: { "${params.outdir}/fastp/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.{html,json}"
],
[
path: { "${params.outdir}/fastp/${meta.id}" },
mode: params.publish_dir_mode,
pattern: "*.fastq.gz",
]
]
ext.prefix = { "${meta.id}_trimmed" }
tag = { "${meta.id}_trim" }
}

withName: MEGAHIT {
ext.args = [
"--k-list ${params.megahit_kmer_list}",
"--min-contig-len ${params.megahit_min_contig_len}"
].join(' ').trim()
publishDir = [
path: { "${params.outdir}/Assembly" },
mode: params.publish_dir_mode,
saveAs: { filename ->
filename.equals('versions.yml')
? null
: filename.indexOf('.contigs.fa.gz') > 0
? filename
: filename.indexOf('.log') > 0 ? filename : null
}
]
ext.prefix = { "${meta.id}_assembled" }
tag = { "${meta.id}_assembly" }
}

withName: BWA_INDEX {
publishDir = [
path: { "${params.outdir}/bwa/index" },
mode: params.publish_dir_mode,
saveAs: { filename ->
if (filename.equals('versions.yml')) return null
return filename.startsWith('bwa/') ? filename.substring(4) : filename
}
]
ext.prefix = { "${meta.id}_index" }
tag = { "${meta.id}_index" }
}

withName: BWA_MEM {
publishDir = [
path: { "${params.outdir}/bwa/aligned" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') ? null : filename
}
]
ext.prefix = { "${meta.id}_aligned" }
tag = { "${meta.id}_align" }
}

withName: SAMTOOLS_SORT {
publishDir = [
path: { "${params.outdir}/samtools/sorted" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename
}
]
ext.prefix = { "${meta.id}_sorted" }
tag = { "${meta.id}_sort" }
}

withName: SAMTOOLS_INDEX {
publishDir = [
path: { "${params.outdir}/samtools/indexed" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename
}
]
ext.prefix = { "${meta.id}_indexed" }
tag = { "${meta.id}_index" }
}

withName: MULTIQC {
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename
}
]
ext.prefix = "multiqc_report"
tag = 'MULTIQC'
}
}
64 changes: 60 additions & 4 deletions workflows/metabolt.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,11 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_meta
include { FASTQC } from '../modules/nf-core/fastqc/main'
include { FASTP } from '../modules/nf-core/fastp/main'
include { MEGAHIT } from '../modules/nf-core/megahit/main'
include { BWA_INDEX } from '../modules/nf-core/bwa/index/main'
include { BWA_MEM } from '../modules/nf-core/bwa/mem/main'
include { SAMTOOLS_SORT } from '../modules/nf-core/samtools/sort/main'
include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/main'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
Expand Down Expand Up @@ -61,20 +66,20 @@ workflow METABOLT {

/*
================================================================================
Assembly and Mapping
Assembly
================================================================================
*/

//
// MODULE: Run MEGAHIT for assembly
//
// Prepare FASTP output for MEGAHIT input
ch_megahit_input = FASTP.out.reads.map { meta, reads ->
def reads1 = meta.single_end ? reads : reads[0]
def reads2 = meta.single_end ? [] : reads[1]
[meta, reads1, reads2]
}

//
// MODULE: Run MEGAHIT for assembly
//
MEGAHIT (
ch_megahit_input
)
Expand All @@ -85,6 +90,55 @@ workflow METABOLT {
[meta + [assembler: 'megahit'], contigs]
}

/*
================================================================================
Mapping and Alignment
================================================================================
*/

//
// MODULE: Run BWA_INDEX on assembled contigs for indexing
//
BWA_INDEX(ch_assemblies)
// Collect version information
ch_versions = ch_versions.mix(BWA_INDEX.out.versions)

//
// MODULE: Run BWA_MEM for alignment of trimmed reads to indexed contigs
//
BWA_MEM(
FASTP.out.reads,
BWA_INDEX.out.index,
ch_assemblies,
true
)
// Collect version information
ch_versions = ch_versions.mix(BWA_MEM.out.versions)

// Prepare input for SAMTOOLS_SORT
ch_bam_for_sort = BWA_MEM.out.bam.map { meta, bam ->
// Ensure meta.id is unique: Add a suffix
[ meta + [id: "${meta.id}_aligned"], bam ]
}
ch_fasta_for_sort = ch_assemblies.map { meta, assembly -> [[id: "assembly"], assembly] }

// SAMTOOLS_SORT
SAMTOOLS_SORT(
ch_bam_for_sort,
ch_fasta_for_sort
)

// Collect version information
ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)

// SAMTOOLS_INDEX
SAMTOOLS_INDEX(SAMTOOLS_SORT.out.bam)
// Collect version information
ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)

// Output channels for downstream use
ch_sorted_bam = SAMTOOLS_SORT.out.bam
ch_bam_index = SAMTOOLS_INDEX.out.bai.mix(SAMTOOLS_INDEX.out.csi)

//
// Collate and save software versions
Expand Down Expand Up @@ -152,6 +206,8 @@ workflow METABOLT {

emit:
assemblies = ch_assemblies // channel:
aligned_sort = ch_sorted_bam
aligned_index = ch_bam_index
multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
versions = ch_versions // channel: [ path(versions.yml) ]

Expand Down

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