mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 07:09:56 +00:00
Install krakenuniq module
This commit is contained in:
parent
4f27998852
commit
36e101a78b
2 changed files with 195 additions and 0 deletions
118
modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
generated
Normal file
118
modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
generated
Normal file
|
@ -0,0 +1,118 @@
|
||||||
|
process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
|
||||||
|
tag "$meta.id"
|
||||||
|
label 'process_high'
|
||||||
|
|
||||||
|
conda (params.enable_conda ? "bioconda::krakenuniq=1.0.0" : null)
|
||||||
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
|
'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.0--pl5321h19e8d03_0':
|
||||||
|
'quay.io/biocontainers/krakenuniq:1.0.0--pl5321h19e8d03_0' }"
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(fastqs)
|
||||||
|
path db
|
||||||
|
val ram_chunk_size
|
||||||
|
val save_output_fastqs
|
||||||
|
val report_file
|
||||||
|
val save_output
|
||||||
|
|
||||||
|
output:
|
||||||
|
tuple val(meta), path('*.classified{.,_}*') , optional:true, emit: classified_reads_fastq
|
||||||
|
tuple val(meta), path('*.unclassified{.,_}*') , optional:true, emit: unclassified_reads_fastq
|
||||||
|
tuple val(meta), path('*classified.txt') , optional:true, emit: classified_assignment
|
||||||
|
tuple val(meta), path('*report.txt') , emit: report
|
||||||
|
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
when:
|
||||||
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
|
script:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
def args2 = task.ext.args ?: ''
|
||||||
|
|
||||||
|
def paired = meta.single_end ? "" : "--paired"
|
||||||
|
def classified = meta.single_end ? '"\$PREFIX".classified.fastq' : '"\$PREFIX".classified#.fastq'
|
||||||
|
def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
|
||||||
|
def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
|
||||||
|
def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
|
||||||
|
def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
|
||||||
|
def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
|
||||||
|
def compress_reads_command = save_output_fastqs ? "gzip --no-name *.fastq" : ""
|
||||||
|
|
||||||
|
"""
|
||||||
|
krakenuniq \\
|
||||||
|
$args \\
|
||||||
|
--db $db \\
|
||||||
|
--preload $ram_chunk_size \\
|
||||||
|
--threads $task.cpus
|
||||||
|
|
||||||
|
for fastq in ${fastqs.join(' ')}; do \\
|
||||||
|
PREFIX=\$(echo \$fastq)
|
||||||
|
krakenuniq \\
|
||||||
|
--db $db \\
|
||||||
|
--threads $task.cpus \\
|
||||||
|
$report \\
|
||||||
|
$output_option \\
|
||||||
|
$unclassified_option \\
|
||||||
|
$classified_option \\
|
||||||
|
$output_option \\
|
||||||
|
$paired \\
|
||||||
|
$args2 \\
|
||||||
|
\$fastq
|
||||||
|
done
|
||||||
|
|
||||||
|
$compress_reads_command
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
|
||||||
|
stub:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
def args2 = task.ext.args ?: ''
|
||||||
|
|
||||||
|
def paired = meta.single_end ? "" : "--paired"
|
||||||
|
def classified = meta.single_end ? '"\$PREFIX".classified.fastq' : '"\$PREFIX".classified#.fastq'
|
||||||
|
def unclassified = meta.single_end ? '"\$PREFIX".unclassified.fastq' : '"\$PREFIX".unclassified#.fastq'
|
||||||
|
def classified_option = save_output_fastqs ? "--classified-out ${classified}" : ""
|
||||||
|
def unclassified_option = save_output_fastqs ? "--unclassified-out ${unclassified}" : ""
|
||||||
|
def output_option = save_output ? '--output "\$PREFIX".krakenuniq.classified.txt' : ""
|
||||||
|
def report = report_file ? '--report-file "\$PREFIX".krakenuniq.report.txt' : ""
|
||||||
|
def compress_reads_command = save_output_fastqs ? "echo 'gzip --no-name *.fastq'" : ""
|
||||||
|
"""
|
||||||
|
echo "krakenuniq \\
|
||||||
|
$args \\
|
||||||
|
--db $db \\
|
||||||
|
--preload $ram_chunk_size \\
|
||||||
|
--threads $task.cpus"
|
||||||
|
|
||||||
|
for fastq in ${fastqs.join(' ')}; do \\
|
||||||
|
PREFIX=\$(echo \$fastq)
|
||||||
|
echo "krakenuniq \\
|
||||||
|
--db $db \\
|
||||||
|
--threads $task.cpus \\
|
||||||
|
$report \\
|
||||||
|
$output_option \\
|
||||||
|
$unclassified_option \\
|
||||||
|
$classified_option \\
|
||||||
|
$output_option \\
|
||||||
|
$paired \\
|
||||||
|
$args2 \\
|
||||||
|
\$fastq"
|
||||||
|
|
||||||
|
touch "\$PREFIX".classified.fastq.gz
|
||||||
|
touch "\$PREFIX".krakenuniq.classified.txt
|
||||||
|
touch "\$PREFIX".krakenuniq.report.txt
|
||||||
|
touch "\$PREFIX".unclassified.fastq.gz
|
||||||
|
done
|
||||||
|
|
||||||
|
$compress_reads_command
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
77
modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
generated
Normal file
77
modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
generated
Normal file
|
@ -0,0 +1,77 @@
|
||||||
|
name: "krakenuniq_preloadedkrakenuniq"
|
||||||
|
description: Classifies metagenomic sequence data using unique k-mer counts
|
||||||
|
keywords:
|
||||||
|
- classify
|
||||||
|
- metagenomics
|
||||||
|
- kmers
|
||||||
|
- fastq
|
||||||
|
- db
|
||||||
|
tools:
|
||||||
|
- "krakenuniq":
|
||||||
|
description: "Metagenomics classifier with unique k-mer counting for more specific results"
|
||||||
|
homepage: https://github.com/fbreitwieser/krakenuniq
|
||||||
|
documentation: https://github.com/fbreitwieser/krakenuniq
|
||||||
|
doi: 10.1186/s13059-018-1568-0
|
||||||
|
licence: ["MIT"]
|
||||||
|
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- fastqs:
|
||||||
|
type: file
|
||||||
|
description: List of input FastQ files
|
||||||
|
- db:
|
||||||
|
type: directory
|
||||||
|
description: KrakenUniq database
|
||||||
|
- ram_chunk_size:
|
||||||
|
type: val
|
||||||
|
description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time
|
||||||
|
pattern: "*GB"
|
||||||
|
- save_output_fastqs:
|
||||||
|
type: boolean
|
||||||
|
description: |
|
||||||
|
If true, optional commands are added to save classified and unclassified reads
|
||||||
|
as fastq files
|
||||||
|
- save_reads_assignment:
|
||||||
|
type: boolean
|
||||||
|
description: |
|
||||||
|
If true, an optional command is added to save a file reporting the taxonomic
|
||||||
|
classification of each input read
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- classified_reads_fastq:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
Reads classified as belonging to any of the taxa
|
||||||
|
on the KrakenUniq database.
|
||||||
|
pattern: "*{fastq.gz}"
|
||||||
|
- unclassified_reads_fastq:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
Reads not classified to any of the taxa
|
||||||
|
on the KrakenUniq database.
|
||||||
|
pattern: "*{fastq.gz}"
|
||||||
|
- classified_assignment:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
KrakenUniq output file indicating the taxonomic assignment of
|
||||||
|
each input read ## DOUBLE CHECK!!
|
||||||
|
- report:
|
||||||
|
type: file
|
||||||
|
description: |
|
||||||
|
KrakenUniq report containing stats about classified
|
||||||
|
and not classifed reads.
|
||||||
|
pattern: "*.{report.txt}"
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
authors:
|
||||||
|
- "@mjamy"
|
Loading…
Reference in a new issue