mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:13:09 +00:00
Merge pull request #77 from genomic-medicine-sweden/add_nanopore_host_reads_removal_with_minimap2
Add nanopore host reads removal with minimap2
This commit is contained in:
commit
e52a40cc9d
17 changed files with 540 additions and 20 deletions
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@ -164,6 +164,47 @@ process {
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]
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]
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}
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}
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withName: MINIMAP2_INDEX {
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ext.args = '-x map-ont'
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publishDir = [
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path: { "${params.outdir}/minimap2/index" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: 'minimap2'
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]
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}
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withName: MINIMAP2_ALIGN {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/minimap2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_mapped,
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pattern: '*.bam'
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]
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}
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withName: SAMTOOLS_VIEW {
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ext.args = '-f 4'
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ext.prefix = { "${meta.id}.mapped.sorted" }
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publishDir = [
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path: { "${params.outdir}/samtools/view" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.bam'
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]
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}
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withName: SAMTOOLS_BAM2FQ {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/samtools/bam2fq" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fq.gz'
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]
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}
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withName: BBMAP_BBDUK {
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withName: BBMAP_BBDUK {
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ext.args = [
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ext.args = [
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"entropy=${params.shortread_complexityfilter_entropy}",
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"entropy=${params.shortread_complexityfilter_entropy}",
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@ -28,7 +28,8 @@ params {
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perform_longread_clip = false
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perform_longread_clip = false
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perform_shortread_complexityfilter = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_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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perform_longread_hostremoval = true
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hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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run_kaiju = true
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run_kaiju = true
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run_kraken2 = true
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run_kraken2 = true
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run_malt = true
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run_malt = true
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@ -191,13 +191,13 @@ You can optionally save the FASTQ output of the run merging with the `--save_com
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#### Host Removal
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#### Host Removal
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Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval`
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Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval` or `--perform_longread_hostremoval`.
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Similarly to complexity filtering, host-removal can be useful for runtime optimisation and reduction in misclassified reads. It is not always necessary to report classification of reads from a host when you already know the host of the sample, therefore you can gain a run-time and computational advantage by removing these prior typically resource-heavy profiling with more efficient methods. Furthermore, particularly with human samples, you can reduce the number of false positives during profiling that occur due to host-sequence contamination in reference genomes on public databases.
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Similarly to complexity filtering, host-removal can be useful for runtime optimisation and reduction in misclassified reads. It is not always necessary to report classification of reads from a host when you already know the host of the sample, therefore you can gain a run-time and computational advantage by removing these prior typically resource-heavy profiling with more efficient methods. Furthermore, particularly with human samples, you can reduce the number of false positives during profiling that occur due to host-sequence contamination in reference genomes on public databases.
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nf-core/taxprofiler currently offers host-removal via alignment against a reference genome with Bowtie2, and the use of the unaligned reads for downstream profiling.
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nf-core/taxprofiler currently offers host-removal via alignment against a reference genome with Bowtie2, and the use of the unaligned reads for downstream profiling.
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You can supply your reference genome in FASTA format with `--shortread_hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used.
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You can supply your reference genome in FASTA format with `--hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index` or `--longread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used.
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> 💡 If you have multiple taxa or sequences you wish to remove (e.g., the host genome and then also PhiX - common quality-control reagent during sequencing) you can simply concatenate the FASTAs of each taxa or sequences into a single reference file.
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> 💡 If you have multiple taxa or sequences you wish to remove (e.g., the host genome and then also PhiX - common quality-control reagent during sequencing) you can simply concatenate the FASTAs of each taxa or sequences into a single reference file.
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|
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12
modules.json
12
modules.json
|
@ -52,6 +52,12 @@
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"git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
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"git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
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},
|
},
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"metaphlan3": {
|
"metaphlan3": {
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"git_sha": "ed4dd1a928ebf4308efb720de878045f7773f8e2"
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},
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"minimap2/align": {
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"git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
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},
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"minimap2/index": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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},
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"multiqc": {
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"multiqc": {
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@ -63,6 +69,12 @@
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"prinseqplusplus": {
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"prinseqplusplus": {
|
||||||
"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
|
"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
|
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},
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},
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"samtools/bam2fq": {
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"git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
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},
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"samtools/view": {
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"git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
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||||||
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},
|
||||||
"untar": {
|
"untar": {
|
||||||
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
|
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
|
||||||
}
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}
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||||||
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2
modules/nf-core/modules/metaphlan3/main.nf
generated
2
modules/nf-core/modules/metaphlan3/main.nf
generated
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@ -23,7 +23,7 @@ process METAPHLAN3 {
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script:
|
script:
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def args = task.ext.args ?: ''
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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 prefix = task.ext.prefix ?: "${meta.id}"
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def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
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def input_type = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
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def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
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def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
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def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
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def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
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||||||
|
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||||||
|
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48
modules/nf-core/modules/minimap2/align/main.nf
generated
Normal file
48
modules/nf-core/modules/minimap2/align/main.nf
generated
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@ -0,0 +1,48 @@
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process MINIMAP2_ALIGN {
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tag "$meta.id"
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label 'process_medium'
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||||||
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conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
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||||||
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
|
'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
|
||||||
|
'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(reads)
|
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|
path reference
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||||||
|
val bam_format
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val cigar_paf_format
|
||||||
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val cigar_bam
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||||||
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|
||||||
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output:
|
||||||
|
tuple val(meta), path("*.paf"), optional: true, emit: paf
|
||||||
|
tuple val(meta), path("*.bam"), optional: true, emit: bam
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
when:
|
||||||
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
|
script:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
|
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
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|
def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
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def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
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def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
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||||||
|
"""
|
||||||
|
minimap2 \\
|
||||||
|
$args \\
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||||||
|
-t $task.cpus \\
|
||||||
|
$reference \\
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||||||
|
$input_reads \\
|
||||||
|
$cigar_paf \\
|
||||||
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$set_cigar_bam \\
|
||||||
|
$bam_output
|
||||||
|
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
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|
"${task.process}":
|
||||||
|
minimap2: \$(minimap2 --version 2>&1)
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
65
modules/nf-core/modules/minimap2/align/meta.yml
generated
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65
modules/nf-core/modules/minimap2/align/meta.yml
generated
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@ -0,0 +1,65 @@
|
||||||
|
name: minimap2_align
|
||||||
|
description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
|
||||||
|
keywords:
|
||||||
|
- align
|
||||||
|
- fasta
|
||||||
|
- fastq
|
||||||
|
- genome
|
||||||
|
- paf
|
||||||
|
- reference
|
||||||
|
tools:
|
||||||
|
- minimap2:
|
||||||
|
description: |
|
||||||
|
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
|
||||||
|
homepage: https://github.com/lh3/minimap2
|
||||||
|
documentation: https://github.com/lh3/minimap2#uguide
|
||||||
|
licence: ["MIT"]
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- reads:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
List of input FASTA or FASTQ files of size 1 and 2 for single-end
|
||||||
|
and paired-end data, respectively.
|
||||||
|
- reference:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
Reference database in FASTA format.
|
||||||
|
- bam_format:
|
||||||
|
type: boolean
|
||||||
|
description: Specify that output should be in BAM format
|
||||||
|
- cigar_paf_format:
|
||||||
|
type: boolean
|
||||||
|
description: Specify that output CIGAR should be in PAF format
|
||||||
|
- cigar_bam:
|
||||||
|
type: boolean
|
||||||
|
description: |
|
||||||
|
Write CIGAR with >65535 ops at the CG tag. This is recommended when
|
||||||
|
doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- paf:
|
||||||
|
type: file
|
||||||
|
description: Alignment in PAF format
|
||||||
|
pattern: "*.paf"
|
||||||
|
- bam:
|
||||||
|
type: file
|
||||||
|
description: Alignment in BAM format
|
||||||
|
pattern: "*.bam"
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
authors:
|
||||||
|
- "@heuermh"
|
||||||
|
- "@sofstam"
|
||||||
|
- "@sateeshperi"
|
||||||
|
- "@jfy133"
|
33
modules/nf-core/modules/minimap2/index/main.nf
generated
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33
modules/nf-core/modules/minimap2/index/main.nf
generated
Normal file
|
@ -0,0 +1,33 @@
|
||||||
|
process MINIMAP2_INDEX {
|
||||||
|
label 'process_medium'
|
||||||
|
|
||||||
|
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
|
||||||
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
|
'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
|
||||||
|
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
|
||||||
|
|
||||||
|
input:
|
||||||
|
path fasta
|
||||||
|
|
||||||
|
output:
|
||||||
|
path "*.mmi" , emit: index
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
when:
|
||||||
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
|
script:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
"""
|
||||||
|
minimap2 \\
|
||||||
|
-t $task.cpus \\
|
||||||
|
-d ${fasta.baseName}.mmi \\
|
||||||
|
$args \\
|
||||||
|
$fasta
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
minimap2: \$(minimap2 --version 2>&1)
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
30
modules/nf-core/modules/minimap2/index/meta.yml
generated
Normal file
30
modules/nf-core/modules/minimap2/index/meta.yml
generated
Normal file
|
@ -0,0 +1,30 @@
|
||||||
|
name: minimap2_index
|
||||||
|
description: Provides fasta index required by minimap2 alignment.
|
||||||
|
keywords:
|
||||||
|
- index
|
||||||
|
- fasta
|
||||||
|
- reference
|
||||||
|
tools:
|
||||||
|
- minimap2:
|
||||||
|
description: |
|
||||||
|
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
|
||||||
|
homepage: https://github.com/lh3/minimap2
|
||||||
|
documentation: https://github.com/lh3/minimap2#uguide
|
||||||
|
licence: ["MIT"]
|
||||||
|
input:
|
||||||
|
- fasta:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
Reference database in FASTA format.
|
||||||
|
output:
|
||||||
|
- mmi:
|
||||||
|
type: file
|
||||||
|
description: Minimap2 fasta index.
|
||||||
|
pattern: "*.mmi"
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
authors:
|
||||||
|
- "@yuukiiwa"
|
||||||
|
- "@drpatelh"
|
56
modules/nf-core/modules/samtools/bam2fq/main.nf
generated
Normal file
56
modules/nf-core/modules/samtools/bam2fq/main.nf
generated
Normal file
|
@ -0,0 +1,56 @@
|
||||||
|
process SAMTOOLS_BAM2FQ {
|
||||||
|
tag "$meta.id"
|
||||||
|
label 'process_low'
|
||||||
|
|
||||||
|
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
|
||||||
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
|
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
|
||||||
|
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(inputbam)
|
||||||
|
val split
|
||||||
|
|
||||||
|
output:
|
||||||
|
tuple val(meta), path("*.fq.gz"), emit: reads
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
when:
|
||||||
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
|
script:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
|
|
||||||
|
if (split){
|
||||||
|
"""
|
||||||
|
samtools \\
|
||||||
|
bam2fq \\
|
||||||
|
$args \\
|
||||||
|
-@ $task.cpus \\
|
||||||
|
-1 ${prefix}_1.fq.gz \\
|
||||||
|
-2 ${prefix}_2.fq.gz \\
|
||||||
|
-0 ${prefix}_other.fq.gz \\
|
||||||
|
-s ${prefix}_singleton.fq.gz \\
|
||||||
|
$inputbam
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
} else {
|
||||||
|
"""
|
||||||
|
samtools \\
|
||||||
|
bam2fq \\
|
||||||
|
$args \\
|
||||||
|
-@ $task.cpus \\
|
||||||
|
$inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
||||||
|
}
|
55
modules/nf-core/modules/samtools/bam2fq/meta.yml
generated
Normal file
55
modules/nf-core/modules/samtools/bam2fq/meta.yml
generated
Normal file
|
@ -0,0 +1,55 @@
|
||||||
|
name: samtools_bam2fq
|
||||||
|
description: |
|
||||||
|
The module uses bam2fq method from samtools to
|
||||||
|
convert a SAM, BAM or CRAM file to FASTQ format
|
||||||
|
keywords:
|
||||||
|
- bam2fq
|
||||||
|
- samtools
|
||||||
|
- fastq
|
||||||
|
tools:
|
||||||
|
- samtools:
|
||||||
|
description: Tools for dealing with SAM, BAM and CRAM files
|
||||||
|
homepage: None
|
||||||
|
documentation: http://www.htslib.org/doc/1.1/samtools.html
|
||||||
|
tool_dev_url: None
|
||||||
|
doi: ""
|
||||||
|
licence: ["MIT"]
|
||||||
|
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- inputbam:
|
||||||
|
type: file
|
||||||
|
description: BAM/CRAM/SAM file
|
||||||
|
pattern: "*.{bam,cram,sam}"
|
||||||
|
- split:
|
||||||
|
type: boolean
|
||||||
|
description: |
|
||||||
|
TRUE/FALSE value to indicate if reads should be separated into
|
||||||
|
/1, /2 and if present other, or singleton.
|
||||||
|
Note: choosing TRUE will generate 4 different files.
|
||||||
|
Choosing FALSE will produce a single file, which will be interleaved in case
|
||||||
|
the input contains paired reads.
|
||||||
|
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
- reads:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
|
||||||
|
or a single interleaved .fq.gz file if the user chooses not to split the reads.
|
||||||
|
pattern: "*.fq.gz"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@lescai"
|
56
modules/nf-core/modules/samtools/view/main.nf
generated
Normal file
56
modules/nf-core/modules/samtools/view/main.nf
generated
Normal file
|
@ -0,0 +1,56 @@
|
||||||
|
process SAMTOOLS_VIEW {
|
||||||
|
tag "$meta.id"
|
||||||
|
label 'process_medium'
|
||||||
|
|
||||||
|
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
|
||||||
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
|
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
|
||||||
|
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(input), path(index)
|
||||||
|
path fasta
|
||||||
|
|
||||||
|
output:
|
||||||
|
tuple val(meta), path("*.bam") , emit: bam , optional: true
|
||||||
|
tuple val(meta), path("*.cram"), emit: cram, optional: true
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
when:
|
||||||
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
|
script:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
def args2 = task.ext.args2 ?: ''
|
||||||
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
|
def reference = fasta ? "--reference ${fasta} -C" : ""
|
||||||
|
def file_type = input.getExtension()
|
||||||
|
if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
|
||||||
|
"""
|
||||||
|
samtools \\
|
||||||
|
view \\
|
||||||
|
--threads ${task.cpus-1} \\
|
||||||
|
${reference} \\
|
||||||
|
$args \\
|
||||||
|
$input \\
|
||||||
|
$args2 \\
|
||||||
|
> ${prefix}.${file_type}
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
|
||||||
|
stub:
|
||||||
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
|
"""
|
||||||
|
touch ${prefix}.bam
|
||||||
|
touch ${prefix}.cram
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
57
modules/nf-core/modules/samtools/view/meta.yml
generated
Normal file
57
modules/nf-core/modules/samtools/view/meta.yml
generated
Normal file
|
@ -0,0 +1,57 @@
|
||||||
|
name: samtools_view
|
||||||
|
description: filter/convert SAM/BAM/CRAM file
|
||||||
|
keywords:
|
||||||
|
- view
|
||||||
|
- bam
|
||||||
|
- sam
|
||||||
|
- cram
|
||||||
|
tools:
|
||||||
|
- samtools:
|
||||||
|
description: |
|
||||||
|
SAMtools is a set of utilities for interacting with and post-processing
|
||||||
|
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
|
||||||
|
These files are generated as output by short read aligners like BWA.
|
||||||
|
homepage: http://www.htslib.org/
|
||||||
|
documentation: hhttp://www.htslib.org/doc/samtools.html
|
||||||
|
doi: 10.1093/bioinformatics/btp352
|
||||||
|
licence: ["MIT"]
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- input:
|
||||||
|
type: file
|
||||||
|
description: BAM/CRAM/SAM file
|
||||||
|
pattern: "*.{bam,cram,sam}"
|
||||||
|
- index:
|
||||||
|
type: optional file
|
||||||
|
description: BAM.BAI/CRAM.CRAI file
|
||||||
|
pattern: "*.{.bai,.crai}"
|
||||||
|
- fasta:
|
||||||
|
type: optional file
|
||||||
|
description: Reference file the CRAM was created with
|
||||||
|
pattern: "*.{fasta,fa}"
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- bam:
|
||||||
|
type: file
|
||||||
|
description: filtered/converted BAM/SAM file
|
||||||
|
pattern: "*.{bam,sam}"
|
||||||
|
- cram:
|
||||||
|
type: file
|
||||||
|
description: filtered/converted CRAM file
|
||||||
|
pattern: "*.cram"
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
authors:
|
||||||
|
- "@drpatelh"
|
||||||
|
- "@joseespinosa"
|
||||||
|
- "@FriederikeHanssen"
|
|
@ -82,12 +82,15 @@ params {
|
||||||
|
|
||||||
// Host Removal
|
// Host Removal
|
||||||
perform_shortread_hostremoval = false
|
perform_shortread_hostremoval = false
|
||||||
shortread_hostremoval_reference = null
|
perform_longread_hostremoval = false
|
||||||
|
hostremoval_reference = null
|
||||||
shortread_hostremoval_index = null
|
shortread_hostremoval_index = null
|
||||||
|
longread_hostremoval_index = null
|
||||||
save_hostremoval_index = false
|
save_hostremoval_index = false
|
||||||
save_hostremoval_mapped = false
|
save_hostremoval_mapped = false
|
||||||
save_hostremoval_unmapped = false
|
save_hostremoval_unmapped = false
|
||||||
|
|
||||||
|
|
||||||
// MALT
|
// MALT
|
||||||
run_malt = false
|
run_malt = false
|
||||||
malt_mode = 'BlastN'
|
malt_mode = 'BlastN'
|
||||||
|
|
|
@ -362,7 +362,10 @@
|
||||||
"perform_shortread_hostremoval": {
|
"perform_shortread_hostremoval": {
|
||||||
"type": "boolean"
|
"type": "boolean"
|
||||||
},
|
},
|
||||||
"shortread_hostremoval_reference": {
|
"perform_longread_hostremoval": {
|
||||||
|
"type": "boolean"
|
||||||
|
},
|
||||||
|
"hostremoval_reference": {
|
||||||
"type": "string",
|
"type": "string",
|
||||||
"default": "None"
|
"default": "None"
|
||||||
},
|
},
|
||||||
|
@ -397,6 +400,10 @@
|
||||||
"type": "string",
|
"type": "string",
|
||||||
"default": "tsv",
|
"default": "tsv",
|
||||||
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
|
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
|
||||||
|
},
|
||||||
|
"longread_hostremoval_index": {
|
||||||
|
"type": "string",
|
||||||
|
"default": "None"
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
47
subworkflows/local/longread_hostremoval.nf
Normal file
47
subworkflows/local/longread_hostremoval.nf
Normal file
|
@ -0,0 +1,47 @@
|
||||||
|
//
|
||||||
|
// Remove host reads via alignment and export off-target reads
|
||||||
|
//
|
||||||
|
|
||||||
|
include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main'
|
||||||
|
include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main'
|
||||||
|
include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main'
|
||||||
|
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main'
|
||||||
|
|
||||||
|
workflow LONGREAD_HOSTREMOVAL {
|
||||||
|
take:
|
||||||
|
reads // [ [ meta ], [ reads ] ]
|
||||||
|
reference // /path/to/fasta
|
||||||
|
index // /path/to/index
|
||||||
|
|
||||||
|
main:
|
||||||
|
ch_versions = Channel.empty()
|
||||||
|
ch_multiqc_files = Channel.empty()
|
||||||
|
|
||||||
|
if ( !params.longread_hostremoval_index ) {
|
||||||
|
ch_minimap2_index = MINIMAP2_INDEX ( reference ).index
|
||||||
|
ch_versions = ch_versions.mix( MINIMAP2_INDEX.out.versions )
|
||||||
|
} else {
|
||||||
|
ch_minimap2_index = index
|
||||||
|
}
|
||||||
|
|
||||||
|
MINIMAP2_ALIGN ( reads, ch_minimap2_index, true, false, false )
|
||||||
|
ch_versions = ch_versions.mix( MINIMAP2_ALIGN.out.versions.first() )
|
||||||
|
ch_minimap2_mapped = MINIMAP2_ALIGN.out.bam
|
||||||
|
.map {
|
||||||
|
meta, reads ->
|
||||||
|
[ meta, reads, [] ]
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
SAMTOOLS_VIEW ( ch_minimap2_mapped , [] )
|
||||||
|
ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
|
||||||
|
|
||||||
|
SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
|
||||||
|
ch_versions = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
|
||||||
|
|
||||||
|
|
||||||
|
emit:
|
||||||
|
reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
|
||||||
|
versions = ch_versions // channel: [ versions.yml ]
|
||||||
|
}
|
||||||
|
|
|
@ -11,7 +11,7 @@ WorkflowTaxprofiler.initialise(params, log)
|
||||||
|
|
||||||
// TODO nf-core: Add all file path parameters for the pipeline to the list below
|
// TODO nf-core: Add all file path parameters for the pipeline to the list below
|
||||||
// Check input path parameters to see if they exist
|
// Check input path parameters to see if they exist
|
||||||
def checkPathParamList = [ params.input, params.databases, params.shortread_hostremoval_reference,
|
def checkPathParamList = [ params.input, params.databases, params.hostremoval_reference,
|
||||||
params.shortread_hostremoval_index, params.multiqc_config
|
params.shortread_hostremoval_index, params.multiqc_config
|
||||||
]
|
]
|
||||||
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
|
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
|
||||||
|
@ -22,11 +22,12 @@ if (params.databases) { ch_databases = file(params.databases) } else { exit 1, '
|
||||||
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_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_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.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
|
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.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_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." }
|
||||||
|
|
||||||
if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) }
|
if (params.hostremoval_reference ) { ch_reference = file(params.hostremoval_reference) }
|
||||||
if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
|
if (params.shortread_hostremoval_index ) { ch_shortread_reference_index = file(params.shortread_hostremoval_index ) } else { ch_shortread_reference_index = [] }
|
||||||
|
if (params.longread_hostremoval_index ) { ch_longread_reference_index = file(params.longread_hostremoval_index ) } else { ch_longread_reference_index = [] }
|
||||||
|
|
||||||
/*
|
/*
|
||||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
@ -52,6 +53,7 @@ include { DB_CHECK } from '../subworkflows/local/db_check'
|
||||||
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
|
include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
|
||||||
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
|
include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
|
||||||
include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
|
include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
|
||||||
|
include { LONGREAD_HOSTREMOVAL } from '../subworkflows/local/longread_hostremoval'
|
||||||
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
include { SHORTREAD_COMPLEXITYFILTERING } from '../subworkflows/local/shortread_complexityfiltering'
|
||||||
include { PROFILING } from '../subworkflows/local/profiling'
|
include { PROFILING } from '../subworkflows/local/profiling'
|
||||||
|
|
||||||
|
@ -141,16 +143,23 @@ workflow TAXPROFILER {
|
||||||
*/
|
*/
|
||||||
|
|
||||||
if ( params.perform_shortread_hostremoval ) {
|
if ( params.perform_shortread_hostremoval ) {
|
||||||
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_reference_index ).reads
|
ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_filtered, ch_reference, ch_shortread_reference_index ).reads
|
||||||
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
|
ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions)
|
||||||
} else {
|
} else {
|
||||||
ch_shortreads_hostremoved = ch_shortreads_filtered
|
ch_shortreads_hostremoved = ch_shortreads_filtered
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if ( params.perform_longread_hostremoval ) {
|
||||||
|
ch_longreads_hostremoved = LONGREAD_HOSTREMOVAL ( ch_longreads_preprocessed, ch_reference, ch_longread_reference_index ).reads
|
||||||
|
ch_versions = ch_versions.mix(LONGREAD_HOSTREMOVAL.out.versions)
|
||||||
|
} else {
|
||||||
|
ch_longreads_hostremoved = ch_longreads_preprocessed
|
||||||
|
}
|
||||||
|
|
||||||
if ( params.perform_runmerging ) {
|
if ( params.perform_runmerging ) {
|
||||||
|
|
||||||
ch_reads_for_cat_branch = ch_shortreads_hostremoved
|
ch_reads_for_cat_branch = ch_shortreads_hostremoved
|
||||||
.mix( ch_longreads_preprocessed )
|
.mix( ch_longreads_hostremoved )
|
||||||
.map {
|
.map {
|
||||||
meta, reads ->
|
meta, reads ->
|
||||||
def meta_new = meta.clone()
|
def meta_new = meta.clone()
|
||||||
|
@ -182,7 +191,7 @@ workflow TAXPROFILER {
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
ch_reads_runmerged = ch_shortreads_hostremoved
|
ch_reads_runmerged = ch_shortreads_hostremoved
|
||||||
.mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
|
.mix( ch_longreads_hostremoved, INPUT_CHECK.out.fasta )
|
||||||
}
|
}
|
||||||
|
|
||||||
/*
|
/*
|
||||||
|
|
Loading…
Reference in a new issue