Merge branch 'dev' into nf-core-template-merge-2.8
James A. Fellows Yates
1 year ago
committed by
GitHub
commit
bca6e645a8
@ -1,3 +1,6 @@
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sample,fastq_1,fastq_2
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||||
SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
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||||
SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
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sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
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2611,ERR5766174,ILLUMINA,,,/<path>/<to>/fasta/ERX5474930_ERR5766174_1.fa.gz
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||||
2612,ERR5766176,ILLUMINA,/<path>/<to>/fastq/ERX5474932_ERR5766176_1.fastq.gz,/<path>/<to>/fastq/ERX5474932_ERR5766176_2.fastq.gz,
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2612,ERR5766180,ILLUMINA,/<path>/<to>/fastq/ERX5474936_ERR5766180_1.fastq.gz,,
|
||||
2613,ERR5766181,ILLUMINA,/<path>/<to>/fastq/ERX5474937_ERR5766181_1.fastq.gz,/<path>/<to>/fastq/ERX5474937_ERR5766181_2.fastq.gz,
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ERR3201952,ERR3201952,OXFORD_NANOPORE,/<path>/<to>/fastq/ERR3201952.fastq.gz,,
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||||
|
@ -0,0 +1,65 @@
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/*
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||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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||||
Nextflow config file for running minimal tests
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Defines input files and everything required to run a fast and simple pipeline test.
|
||||
|
||||
Use as follows:
|
||||
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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||||
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||||
----------------------------------------------------------------------------------------
|
||||
*/
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||||
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||||
//
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||||
// Separate test as KrakenUniq database can sometimes be too big for GHA
|
||||
//
|
||||
|
||||
params {
|
||||
config_profile_name = 'Test profile'
|
||||
config_profile_description = 'Minimal test to check KrakenUniq function'
|
||||
|
||||
// Limit resources so that this can run on GitHub Actions
|
||||
max_cpus = 2
|
||||
max_memory = '6.GB'
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||||
max_time = '6.h'
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||||
|
||||
// Input data
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||||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_krakenuniq.csv'
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||||
perform_shortread_qc = true
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||||
perform_longread_qc = true
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||||
shortread_qc_mergepairs = true
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||||
perform_shortread_complexityfilter = true
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||||
perform_shortread_hostremoval = true
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||||
perform_longread_hostremoval = true
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||||
perform_runmerging = 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 = false
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||||
run_kraken2 = false
|
||||
run_bracken = false
|
||||
run_malt = false
|
||||
run_metaphlan3 = false
|
||||
run_centrifuge = false
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||||
run_diamond = false
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run_krakenuniq = true
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||||
run_motus = false
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||||
run_krona = true
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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malt_save_reads = false
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||||
kraken2_save_reads = false
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||||
centrifuge_save_reads = false
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||||
diamond_save_reads = false
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run_profile_standardisation = true
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||||
}
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||||
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process {
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||||
withName: MALT_RUN {
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maxForks = 1
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}
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withName: MEGAN_RMA2INFO_TSV {
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||||
maxForks = 1
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||||
}
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||||
withName: MEGAN_RMA2INFO_KRONA {
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||||
maxForks = 1
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||||
}
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||||
}
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||||
@ -0,0 +1,49 @@
|
||||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Nextflow config file for running minimal tests
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Defines input files and everything required to run a fast and simple pipeline test.
|
||||
|
||||
Use as follows:
|
||||
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
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||||
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||||
----------------------------------------------------------------------------------------
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||||
*/
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||||
//
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||||
// Separate test as mOTUs database download can be flaky
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||||
//
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params {
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||||
config_profile_name = 'mOTUs Test profile'
|
||||
config_profile_description = 'Minimal test to check mOTUs function'
|
||||
|
||||
// Limit resources so that this can run on GitHub Actions
|
||||
max_cpus = 2
|
||||
max_memory = '6.GB'
|
||||
max_time = '6.h'
|
||||
|
||||
// Input data
|
||||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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||||
databases = 'database_motus.csv'
|
||||
perform_shortread_qc = false
|
||||
perform_longread_qc = false
|
||||
perform_shortread_complexityfilter = false
|
||||
perform_shortread_hostremoval = false
|
||||
perform_longread_hostremoval = false
|
||||
perform_runmerging = false
|
||||
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||
run_kaiju = false
|
||||
run_kraken2 = false
|
||||
run_bracken = false
|
||||
run_malt = false
|
||||
run_metaphlan3 = false
|
||||
run_centrifuge = false
|
||||
run_diamond = false
|
||||
run_krakenuniq = false
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||||
run_motus = true
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||||
motus_save_mgc_read_counts = false
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||||
motus_remove_ncbi_ids = false
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||||
motus_use_relative_abundance = false
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||||
run_profile_standardisation = true
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||||
}
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||||
@ -0,0 +1,49 @@
|
||||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Nextflow config file for running minimal tests
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Defines input files and everything required to run a fast and simple pipeline test.
|
||||
|
||||
Use as follows:
|
||||
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
|
||||
|
||||
----------------------------------------------------------------------------------------
|
||||
*/
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||||
|
||||
params {
|
||||
config_profile_name = 'Test profile'
|
||||
config_profile_description = 'Minimal test dataset skipping all preprocessing to check pipeline function'
|
||||
|
||||
// Limit resources so that this can run on GitHub Actions
|
||||
max_cpus = 2
|
||||
max_memory = '6.GB'
|
||||
max_time = '6.h'
|
||||
|
||||
// Input data
|
||||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
|
||||
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
|
||||
perform_shortread_qc = false
|
||||
perform_longread_qc = false
|
||||
perform_shortread_complexityfilter = false
|
||||
perform_shortread_hostremoval = false
|
||||
perform_longread_hostremoval = false
|
||||
perform_runmerging = false
|
||||
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||
run_kaiju = true
|
||||
run_kraken2 = true
|
||||
run_bracken = true
|
||||
run_malt = true
|
||||
run_metaphlan3 = true
|
||||
run_centrifuge = true
|
||||
run_diamond = true
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||||
run_krakenuniq = true
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||||
run_motus = false
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||||
run_krona = true
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||||
}
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||||
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||||
process {
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||||
withName: MALT_RUN {
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||||
maxForks = 1
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||||
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
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||||
}
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||||
}
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||||
@ -0,0 +1,48 @@
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||||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Nextflow config file for running minimal tests
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Defines input files and everything required to run a fast and simple pipeline test.
|
||||
|
||||
Use as follows:
|
||||
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
|
||||
|
||||
----------------------------------------------------------------------------------------
|
||||
*/
|
||||
|
||||
params {
|
||||
config_profile_name = 'Test profile'
|
||||
config_profile_description = 'Minimal test dataset without performing any profiling to check pipeline function'
|
||||
|
||||
// Limit resources so that this can run on GitHub Actions
|
||||
max_cpus = 2
|
||||
max_memory = '6.GB'
|
||||
max_time = '6.h'
|
||||
|
||||
// Input data
|
||||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
|
||||
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
|
||||
perform_shortread_qc = true
|
||||
perform_longread_qc = true
|
||||
shortread_qc_mergepairs = true
|
||||
perform_shortread_complexityfilter = true
|
||||
perform_shortread_hostremoval = true
|
||||
perform_longread_hostremoval = true
|
||||
perform_runmerging = true
|
||||
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||
run_kaiju = false
|
||||
run_kraken2 = false
|
||||
run_bracken = false
|
||||
run_malt = false
|
||||
run_metaphlan3 = false
|
||||
run_centrifuge = false
|
||||
run_diamond = false
|
||||
run_krakenuniq = false
|
||||
run_motus = false
|
||||
}
|
||||
|
||||
process {
|
||||
withName: MALT_RUN {
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||||
maxForks = 1
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||||
}
|
||||
}
|
||||
@ -0,0 +1,48 @@
|
||||
/*
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Nextflow config file for running minimal tests
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
Defines input files and everything required to run a fast and simple pipeline test.
|
||||
|
||||
Use as follows:
|
||||
nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
|
||||
|
||||
----------------------------------------------------------------------------------------
|
||||
*/
|
||||
|
||||
params {
|
||||
config_profile_name = 'Test profile'
|
||||
config_profile_description = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others"
|
||||
|
||||
// Limit resources so that this can run on GitHub Actions
|
||||
max_cpus = 2
|
||||
max_memory = '6.GB'
|
||||
max_time = '6.h'
|
||||
|
||||
// Input data
|
||||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
|
||||
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
|
||||
perform_shortread_qc = false
|
||||
perform_longread_qc = false
|
||||
perform_shortread_complexityfilter = false
|
||||
perform_shortread_hostremoval = false
|
||||
perform_longread_hostremoval = false
|
||||
perform_runmerging = false
|
||||
hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
|
||||
run_kaiju = false
|
||||
run_kraken2 = false
|
||||
run_bracken = false
|
||||
run_malt = false
|
||||
run_metaphlan3 = false
|
||||
run_centrifuge = false
|
||||
run_diamond = false
|
||||
run_krakenuniq = false
|
||||
run_motus = false
|
||||
}
|
||||
|
||||
process {
|
||||
withName: MALT_RUN {
|
||||
maxForks = 1
|
||||
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
|
||||
}
|
||||
}
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||||
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@ -0,0 +1,32 @@
|
||||
process KRAKEN2_STANDARD_REPORT {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "conda-forge::sed=4.7"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
|
||||
'ubuntu:20.04' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
|
||||
output:
|
||||
tuple val(meta), path(result), emit: report
|
||||
path 'versions.yml' , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
result = "${prefix}_standardized.kraken2.report.txt"
|
||||
"""
|
||||
cut -f1-3,6-8 '${report}' > '${result}'
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cut: \$(echo \$(cut --version 2>&1) | sed 's/^.*(GNU coreutils) //; s/ Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
@ -0,0 +1,40 @@
|
||||
process KRONA_CLEANUP {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda "conda-forge::sed=4.7"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
|
||||
'ubuntu:20.04' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: txt
|
||||
path "versions.yml", emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
# Copy the file to a new name
|
||||
cp ${krona} ${prefix}.txt
|
||||
|
||||
# Remove ugly 'x__' prefixes for each of the taxonomic levels
|
||||
LEVELS=(d k p c o f g s)
|
||||
for L in "\${LEVELS[@]}"; do
|
||||
sed -i "s/\${L}__//g" ${prefix}.txt
|
||||
done
|
||||
|
||||
# Remove underscores that are standing in place of spaces
|
||||
sed -i "s/_/ /g" ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,92 @@
|
||||
process ADAPTERREMOVAL {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda "bioconda::adapterremoval=2.3.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
|
||||
'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path(adapterlist)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
|
||||
tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
|
||||
tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
|
||||
tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
|
||||
tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
|
||||
tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
|
||||
tuple val(meta), path('*.settings') , emit: settings
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def list = adapterlist ? "--adapter-list ${adapterlist}" : ""
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
AdapterRemoval \\
|
||||
--file1 $reads \\
|
||||
$args \\
|
||||
$list \\
|
||||
--basename ${prefix} \\
|
||||
--threads ${task.cpus} \\
|
||||
--seed 42 \\
|
||||
--gzip
|
||||
|
||||
ensure_fastq() {
|
||||
if [ -f "\${1}" ]; then
|
||||
mv "\${1}" "\${1::-3}.fastq.gz"
|
||||
fi
|
||||
|
||||
}
|
||||
|
||||
ensure_fastq '${prefix}.truncated.gz'
|
||||
ensure_fastq '${prefix}.discarded.gz'
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
AdapterRemoval \\
|
||||
--file1 ${reads[0]} \\
|
||||
--file2 ${reads[1]} \\
|
||||
$args \\
|
||||
$list \\
|
||||
--basename ${prefix} \\
|
||||
--threads $task.cpus \\
|
||||
--seed 42 \\
|
||||
--gzip
|
||||
|
||||
ensure_fastq() {
|
||||
if [ -f "\${1}" ]; then
|
||||
mv "\${1}" "\${1::-3}.fastq.gz"
|
||||
fi
|
||||
|
||||
}
|
||||
|
||||
ensure_fastq '${prefix}.truncated.gz'
|
||||
ensure_fastq '${prefix}.discarded.gz'
|
||||
ensure_fastq '${prefix}.pair1.truncated.gz'
|
||||
ensure_fastq '${prefix}.pair2.truncated.gz'
|
||||
ensure_fastq '${prefix}.collapsed.gz'
|
||||
ensure_fastq '${prefix}.collapsed.truncated.gz'
|
||||
ensure_fastq '${prefix}.paired.gz'
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,90 @@
|
||||
name: adapterremoval
|
||||
description: Trim sequencing adapters and collapse overlapping reads
|
||||
keywords:
|
||||
- trimming
|
||||
- adapters
|
||||
- merging
|
||||
- fastq
|
||||
tools:
|
||||
- adapterremoval:
|
||||
description: The AdapterRemoval v2 tool for merging and clipping reads.
|
||||
homepage: https://github.com/MikkelSchubert/adapterremoval
|
||||
documentation: https://adapterremoval.readthedocs.io
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
|
||||
- adapterlist:
|
||||
type: file
|
||||
description: Optional text file containing list of adapters to look for for removal
|
||||
with one adapter per line. Otherwise will look for default adapters (see
|
||||
AdapterRemoval man page), or can be modified to remove user-specified
|
||||
adapters via ext.args.
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- singles_truncated:
|
||||
type: file
|
||||
description: |
|
||||
Adapter trimmed FastQ files of either single-end reads, or singleton
|
||||
'orphaned' reads from merging of paired-end data (i.e., one of the pair
|
||||
was lost due to filtering thresholds).
|
||||
pattern: "*.truncated.fastq.gz"
|
||||
- discarded:
|
||||
type: file
|
||||
description: |
|
||||
Adapter trimmed FastQ files of reads that did not pass filtering
|
||||
thresholds.
|
||||
pattern: "*.discarded.fastq.gz"
|
||||
- pair1_truncated:
|
||||
type: file
|
||||
description: |
|
||||
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
|
||||
with their respective R2 pair due to long templates. The respective pair
|
||||
is stored in 'pair2_truncated'.
|
||||
pattern: "*.pair1.truncated.fastq.gz"
|
||||
- pair2_truncated:
|
||||
type: file
|
||||
description: |
|
||||
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
|
||||
with their respective R1 pair due to long templates. The respective pair
|
||||
is stored in 'pair1_truncated'.
|
||||
pattern: "*.pair2.truncated.fastq.gz"
|
||||
- collapsed:
|
||||
type: file
|
||||
description: |
|
||||
Collapsed FastQ of paired-end reads that successfully merged with their
|
||||
respective R1 pair but were not trimmed.
|
||||
pattern: "*.collapsed.fastq.gz"
|
||||
- collapsed_truncated:
|
||||
type: file
|
||||
description: |
|
||||
Collapsed FastQ of paired-end reads that successfully merged with their
|
||||
respective R1 pair and were trimmed of adapter due to sufficient overlap.
|
||||
pattern: "*.collapsed.truncated.fastq.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: AdapterRemoval log file
|
||||
pattern: "*.settings"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@maxibor"
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,43 @@
|
||||
process BBMAP_BBDUK {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda "bioconda::bbmap=39.01"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0':
|
||||
'quay.io/biocontainers/bbmap:39.01--h5c4e2a8_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path contaminants
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.fastq.gz'), emit: reads
|
||||
tuple val(meta), path('*.log') , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
|
||||
def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
|
||||
def contaminants_fa = contaminants ? "ref=$contaminants" : ''
|
||||
"""
|
||||
maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
|
||||
bbduk.sh \\
|
||||
-Xmx\$maxmem \\
|
||||
$raw \\
|
||||
$trimmed \\
|
||||
threads=$task.cpus \\
|
||||
$args \\
|
||||
$contaminants_fa \\
|
||||
&> ${prefix}.bbduk.log
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,53 @@
|
||||
name: bbmap_bbduk
|
||||
description: Adapter and quality trimming of sequencing reads
|
||||
keywords:
|
||||
- trimming
|
||||
- adapter trimming
|
||||
- quality trimming
|
||||
- fastq
|
||||
tools:
|
||||
- bbmap:
|
||||
description: BBMap is a short read aligner, as well as various other bioinformatic tools.
|
||||
homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- contaminants:
|
||||
type: file
|
||||
description: |
|
||||
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: The trimmed/modified fastq reads
|
||||
pattern: "*fastq.gz"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- log:
|
||||
type: file
|
||||
description: Bbduk log file
|
||||
pattern: "*bbduk.log"
|
||||
|
||||
authors:
|
||||
- "@MGordon09"
|
||||
@ -0,0 +1,71 @@
|
||||
process BOWTIE2_ALIGN {
|
||||
tag "$meta.id"
|
||||
label "process_high"
|
||||
|
||||
conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
|
||||
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta) , path(reads)
|
||||
tuple val(meta2), path(index)
|
||||
val save_unaligned
|
||||
val sort_bam
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam") , emit: bam
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
tuple val(meta), path("*fastq.gz"), emit: fastq, 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 unaligned = ""
|
||||
def reads_args = ""
|
||||
if (meta.single_end) {
|
||||
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
|
||||
reads_args = "-U ${reads}"
|
||||
} else {
|
||||
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
|
||||
reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
|
||||
}
|
||||
|
||||
def samtools_command = sort_bam ? 'sort' : 'view'
|
||||
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
|
||||
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
|
||||
[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
|
||||
|
||||
bowtie2 \\
|
||||
-x \$INDEX \\
|
||||
$reads_args \\
|
||||
--threads $task.cpus \\
|
||||
$unaligned \\
|
||||
$args \\
|
||||
2> ${prefix}.bowtie2.log \\
|
||||
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
|
||||
|
||||
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
|
||||
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
|
||||
fi
|
||||
|
||||
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
|
||||
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
|
||||
fi
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,67 @@
|
||||
name: bowtie2_align
|
||||
description: Align reads to a reference genome using bowtie2
|
||||
keywords:
|
||||
- align
|
||||
- map
|
||||
- fasta
|
||||
- fastq
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- meta2:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing reference information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.ebwt"
|
||||
- save_unaligned:
|
||||
type: boolean
|
||||
description: |
|
||||
Save reads that do not map to the reference (true) or discard them (false)
|
||||
(default: false)
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: Aligment log
|
||||
pattern: "*.log"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
@ -0,0 +1,30 @@
|
||||
process BOWTIE2_BUILD {
|
||||
tag "$fasta"
|
||||
label 'process_high'
|
||||
|
||||
conda "bioconda::bowtie2=2.4.4"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
|
||||
'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path('bowtie2') , emit: index
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
mkdir bowtie2
|
||||
bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,43 @@
|
||||
name: bowtie2_build
|
||||
description: Builds bowtie index for reference genome
|
||||
keywords:
|
||||
- build
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing reference information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing reference information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.bt2"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
@ -0,0 +1,42 @@
|
||||
process BRACKEN_BRACKEN {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
// WARN: Version information not provided by tool on CLI.
|
||||
// Please update version string below when bumping container versions.
|
||||
conda "bioconda::bracken=2.7"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
|
||||
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(kraken_report)
|
||||
path database
|
||||
|
||||
output:
|
||||
tuple val(meta), path(bracken_report), emit: reports
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ""
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
bracken_report = "${prefix}.tsv"
|
||||
// WARN: Version information not provided by tool on CLI.
|
||||
// Please update version string below when bumping container versions.
|
||||
def VERSION = '2.7'
|
||||
"""
|
||||
bracken \\
|
||||
${args} \\
|
||||
-d '${database}' \\
|
||||
-i '${kraken_report}' \\
|
||||
-o '${bracken_report}'
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bracken: ${VERSION}
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,48 @@
|
||||
name: bracken_bracken
|
||||
description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
|
||||
keywords:
|
||||
- bracken
|
||||
- metagenomics
|
||||
- abundance
|
||||
- kraken2
|
||||
tools:
|
||||
- bracken:
|
||||
description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
|
||||
homepage: https://ccb.jhu.edu/software/bracken/
|
||||
documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
|
||||
tool_dev_url: https://github.com/jenniferlu717/Bracken
|
||||
doi: "10.7717/peerj-cs.104"
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- kraken_report:
|
||||
type: file
|
||||
description: TSV file with six columns coming from kraken2 output
|
||||
pattern: "*.{tsv}"
|
||||
- database:
|
||||
type: file
|
||||
description: Directory containing the kraken2/Bracken files for analysis
|
||||
pattern: "*"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- reports:
|
||||
type: file
|
||||
description: TSV output report of the re-estimated abundances
|
||||
pattern: "*.{tsv}"
|
||||
|
||||
authors:
|
||||
- "@Midnighter"
|
||||
@ -0,0 +1,37 @@
|
||||
process BRACKEN_COMBINEBRACKENOUTPUTS {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda "bioconda::bracken=2.7"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
|
||||
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: txt
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
// WARN: Version information not provided by tool on CLI.
|
||||
// Please update version string below when bumping container versions.
|
||||
def VERSION = '2.7'
|
||||
"""
|
||||
combine_bracken_outputs.py \\
|
||||
$args \\
|
||||
--files ${input} \\
|
||||
-o ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
combine_bracken_output: ${VERSION}
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,41 @@
|
||||
name: "bracken_combinebrackenoutputs"
|
||||
description: Combine output of metagenomic samples analyzed by bracken.
|
||||
keywords:
|
||||
- sort
|
||||
tools:
|
||||
- "bracken":
|
||||
description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
|
||||
homepage: https://ccb.jhu.edu/software/bracken/
|
||||
documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
|
||||
tool_dev_url: https://github.com/jenniferlu717/Bracken
|
||||
doi: "10.7717/peerj-cs.104"
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- input:
|
||||
type: file
|
||||
description: List of output files from bracken
|
||||
pattern: "*"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- txt:
|
||||
type: file
|
||||
description: Combined output in table format
|
||||
pattern: "*.txt"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,80 @@
|
||||
process CAT_FASTQ {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "conda-forge::sed=4.7"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
|
||||
'ubuntu:20.04' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads, stageAs: "input*/*")
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.merged.fastq.gz"), emit: reads
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
|
||||
if (meta.single_end) {
|
||||
if (readList.size >= 1) {
|
||||
"""
|
||||
cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
} else {
|
||||
if (readList.size >= 2) {
|
||||
def read1 = []
|
||||
def read2 = []
|
||||
readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
|
||||
"""
|
||||
cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
|
||||
cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
||||
|
||||
stub:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
|
||||
if (meta.single_end) {
|
||||
if (readList.size > 1) {
|
||||
"""
|
||||
touch ${prefix}.merged.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
} else {
|
||||
if (readList.size > 2) {
|
||||
"""
|
||||
touch ${prefix}_1.merged.fastq.gz
|
||||
touch ${prefix}_2.merged.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1,39 @@
|
||||
name: cat_fastq
|
||||
description: Concatenates fastq files
|
||||
keywords:
|
||||
- fastq
|
||||
- concatenate
|
||||
tools:
|
||||
- cat:
|
||||
description: |
|
||||
The cat utility reads files sequentially, writing them to the standard output.
|
||||
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: list
|
||||
description: |
|
||||
List of input FastQ files to be concatenated.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: Merged fastq file
|
||||
pattern: "*.{merged.fastq.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
@ -0,0 +1,61 @@
|
||||
process CENTRIFUGE_CENTRIFUGE {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda "bioconda::centrifuge=1.0.4_beta"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
|
||||
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path db
|
||||
val save_unaligned
|
||||
val save_aligned
|
||||
val sam_format
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*report.txt') , emit: report
|
||||
tuple val(meta), path('*results.txt') , emit: results
|
||||
tuple val(meta), path('*.sam') , optional: true, emit: sam
|
||||
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
|
||||
tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
|
||||
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 paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
|
||||
def unaligned = ''
|
||||
def aligned = ''
|
||||
if (meta.single_end) {
|
||||
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
|
||||
} else {
|
||||
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
|
||||
}
|
||||
def sam_output = sam_format ? "--out-fmt 'sam'" : ''
|
||||
"""
|
||||
## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
|
||||
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/\\.1.cf\$//'`
|
||||
centrifuge \\
|
||||
-x \$db_name \\
|
||||
-p $task.cpus \\
|
||||
$paired \\
|
||||
--report-file ${prefix}.report.txt \\
|
||||
-S ${prefix}.results.txt \\
|
||||
$unaligned \\
|
||||
$aligned \\
|
||||
$sam_output \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,66 @@
|
||||
name: centrifuge_centrifuge
|
||||
description: Classifies metagenomic sequence data
|
||||
keywords:
|
||||
- classify
|
||||
- metagenomics
|
||||
- fastq
|
||||
- db
|
||||
tools:
|
||||
- centrifuge:
|
||||
description: Centrifuge is a classifier for metagenomic sequences.
|
||||
homepage: https://ccb.jhu.edu/software/centrifuge/
|
||||
documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
|
||||
doi: 10.1101/gr.210641.116
|
||||
licence: ["GPL v3"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- db:
|
||||
type: directory
|
||||
description: Path to directory containing centrifuge database files
|
||||
- save_unaligned:
|
||||
type: value
|
||||
description: If true unmapped fastq files are saved
|
||||
- save_aligned:
|
||||
type: value
|
||||
description: If true mapped fastq files are saved
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: |
|
||||
File containing a classification summary
|
||||
pattern: "*.{report.txt}"
|
||||
- results:
|
||||
type: file
|
||||
description: |
|
||||
File containing classification results
|
||||
pattern: "*.{results.txt}"
|
||||
- fastq_unmapped:
|
||||
type: file
|
||||
description: Unmapped fastq files
|
||||
pattern: "*.unmapped.fastq.gz"
|
||||
- fastq_mapped:
|
||||
type: file
|
||||
description: Mapped fastq files
|
||||
pattern: "*.mapped.fastq.gz"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@sofstam"
|
||||
- "@jfy133"
|
||||
- "@sateeshperi"
|
||||
@ -0,0 +1,33 @@
|
||||
process CENTRIFUGE_KREPORT {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::centrifuge=1.0.4_beta"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6':
|
||||
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
path db
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.txt') , emit: kreport
|
||||
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}"
|
||||
"""
|
||||
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/\\.1.cf\$//'`
|
||||
centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,41 @@
|
||||
name: "centrifuge_kreport"
|
||||
description: Creates Kraken-style reports from centrifuge out files
|
||||
keywords:
|
||||
- metagenomics
|
||||
tools:
|
||||
- centrifuge:
|
||||
description: Centrifuge is a classifier for metagenomic sequences.
|
||||
homepage: https://ccb.jhu.edu/software/centrifuge/
|
||||
documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
|
||||
doi: 10.1101/gr.210641.116
|
||||
licence: ["GPL v3"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: File containing the centrifuge classification report
|
||||
pattern: "*.{txt}"
|
||||
|
||||
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"
|
||||
- kreport:
|
||||
type: file
|
||||
description: |
|
||||
File containing kraken-style report from centrifuge
|
||||
out files.
|
||||
pattern: "*.{txt}"
|
||||
authors:
|
||||
- "@sofstam"
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,68 @@
|
||||
process DIAMOND_BLASTX {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda "bioconda::diamond=2.0.15"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
|
||||
'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
path db
|
||||
val out_ext
|
||||
val blast_columns
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.blast'), optional: true, emit: blast
|
||||
tuple val(meta), path('*.xml') , optional: true, emit: xml
|
||||
tuple val(meta), path('*.txt') , optional: true, emit: txt
|
||||
tuple val(meta), path('*.daa') , optional: true, emit: daa
|
||||
tuple val(meta), path('*.sam') , optional: true, emit: sam
|
||||
tuple val(meta), path('*.tsv') , optional: true, emit: tsv
|
||||
tuple val(meta), path('*.paf') , optional: true, emit: paf
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def columns = blast_columns ? "${blast_columns}" : ''
|
||||
switch ( out_ext ) {
|
||||
case "blast": outfmt = 0; break
|
||||
case "xml": outfmt = 5; break
|
||||
case "txt": outfmt = 6; break
|
||||
case "daa": outfmt = 100; break
|
||||
case "sam": outfmt = 101; break
|
||||
case "tsv": outfmt = 102; break
|
||||
case "paf": outfmt = 103; break
|
||||
default:
|
||||
outfmt = '6';
|
||||
out_ext = 'txt';
|
||||
log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
|
||||
break
|
||||
}
|
||||
"""
|
||||
DB=`find -L ./ -name "*.dmnd" | sed 's/\\.dmnd\$//'`
|
||||
|
||||
diamond \\
|
||||
blastx \\
|
||||
--threads $task.cpus \\
|
||||
--db \$DB \\
|
||||
--query $fasta \\
|
||||
--outfmt ${outfmt} ${columns} \\
|
||||
$args \\
|
||||
--out ${prefix}.${out_ext} \\
|
||||
--log
|
||||
|
||||
mv diamond.log ${prefix}.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
diamond: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,81 @@
|
||||
name: diamond_blastx
|
||||
description: Queries a DIAMOND database using blastx mode
|
||||
keywords:
|
||||
- fasta
|
||||
- diamond
|
||||
- blastx
|
||||
- DNA sequence
|
||||
tools:
|
||||
- diamond:
|
||||
description: Accelerated BLAST compatible local sequence aligner
|
||||
homepage: https://github.com/bbuchfink/diamond
|
||||
documentation: https://github.com/bbuchfink/diamond/wiki
|
||||
tool_dev_url: https://github.com/bbuchfink/diamond
|
||||
doi: "doi:10.1038/s41592-021-01101-x"
|
||||
licence: ["GPL v3.0"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file containing query sequences
|
||||
pattern: "*.{fa,fasta}"
|
||||
- db:
|
||||
type: directory
|
||||
description: Directory containing the nucelotide blast database
|
||||
pattern: "*"
|
||||
- out_ext:
|
||||
type: string
|
||||
description: |
|
||||
Specify the type of output file to be generated. `blast` corresponds to
|
||||
BLAST pairwise format. `xml` corresponds to BLAST xml format.
|
||||
`txt` corresponds to to BLAST tabular format. `tsv` corresponds to
|
||||
taxonomic classification format.
|
||||
pattern: "blast|xml|txt|daa|sam|tsv|paf"
|
||||
|
||||
output:
|
||||
- blast:
|
||||
type: file
|
||||
description: File containing blastp hits
|
||||
pattern: "*.{blast}"
|
||||
- xml:
|
||||
type: file
|
||||
description: File containing blastp hits
|
||||
pattern: "*.{xml}"
|
||||
- txt:
|
||||
type: file
|
||||
description: File containing hits in tabular BLAST format.
|
||||
pattern: "*.{txt}"
|
||||
- daa:
|
||||
type: file
|
||||
description: File containing hits DAA format
|
||||
pattern: "*.{daa}"
|
||||
- sam:
|
||||
type: file
|
||||
description: File containing aligned reads in SAM format
|
||||
pattern: "*.{sam}"
|
||||
- tsv:
|
||||
type: file
|
||||
description: Tab separated file containing taxonomic classification of hits
|
||||
pattern: "*.{tsv}"
|
||||
- paf:
|
||||
type: file
|
||||
description: File containing aligned reads in pairwise mapping format format
|
||||
pattern: "*.{paf}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- log:
|
||||
type: file
|
||||
description: Log file containing stdout information
|
||||
pattern: "*.{log}"
|
||||
|
||||
authors:
|
||||
- "@spficklin"
|
||||
- "@jfy133"
|
||||
- "@mjamy"
|
||||
@ -0,0 +1,16 @@
|
||||
Changes in module 'nf-core/falco'
|
||||
--- modules/nf-core/falco/main.nf
|
||||
+++ modules/nf-core/falco/main.nf
|
||||
@@ -33,7 +33,9 @@
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
- falco $args --threads $task.cpus ${reads}
|
||||
+ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||
+ [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||
+ falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
||||
************************************************************
|
||||
@ -0,0 +1,59 @@
|
||||
process FALCO {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
|
||||
conda "bioconda::falco=1.2.1"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3':
|
||||
'quay.io/biocontainers/falco:1.2.1--h867801b_3' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.html"), emit: html
|
||||
tuple val(meta), path("*.txt") , emit: txt
|
||||
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 ( reads.toList().size() == 1 ) {
|
||||
"""
|
||||
falco $args --threads $task.cpus ${reads} -D ${prefix}_data.txt -S ${prefix}_summary.txt -R ${prefix}_report.html
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
falco:\$( falco --version | sed -e "s/falco//g" )
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||
falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
falco:\$( falco --version | sed -e "s/falco//g" )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
stub:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
touch ${prefix}_data.txt
|
||||
touch ${prefix}_fastqc_data.html
|
||||
touch ${prefix}_summary.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
falco: \$( falco --version | sed -e "s/falco v//g" )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,52 @@
|
||||
name: falco
|
||||
description: Run falco on sequenced reads
|
||||
keywords:
|
||||
- quality control
|
||||
- qc
|
||||
- adapters
|
||||
- fastq
|
||||
tools:
|
||||
- fastqc:
|
||||
description: "falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads."
|
||||
|
||||
homepage: "https://falco.readthedocs.io/"
|
||||
documentation: "https://falco.readthedocs.io/"
|
||||
tool_dev_url: "None"
|
||||
doi: ""
|
||||
licence: "['GPL v3']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- html:
|
||||
type: file
|
||||
description: FastQC like report
|
||||
pattern: "*_{fastqc_report.html}"
|
||||
- txt:
|
||||
type: file
|
||||
description: falco report data
|
||||
pattern: "*_{data.txt}"
|
||||
- txt:
|
||||
type: file
|
||||
description: falco summary file
|
||||
pattern: "*_{summary.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@lucacozzuto"
|
||||
@ -0,0 +1,103 @@
|
||||
process FASTP {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda "bioconda::fastp=0.23.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
|
||||
'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path adapter_fasta
|
||||
val save_trimmed_fail
|
||||
val save_merged
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.fastp.fastq.gz') , optional:true, emit: reads
|
||||
tuple val(meta), path('*.json') , emit: json
|
||||
tuple val(meta), path('*.html') , emit: html
|
||||
tuple val(meta), path('*.log') , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail
|
||||
tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def adapter_list = adapter_fasta ? "--adapter_fasta ${adapter_fasta}" : ""
|
||||
def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
|
||||
// Added soft-links to original fastqs for consistent naming in MultiQC
|
||||
// Use single ended for interleaved. Add --interleaved_in in config.
|
||||
if ( task.ext.args?.contains('--interleaved_in') ) {
|
||||
"""
|
||||
[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
|
||||
|
||||
fastp \\
|
||||
--stdout \\
|
||||
--in1 ${prefix}.fastq.gz \\
|
||||
--thread $task.cpus \\
|
||||
--json ${prefix}.fastp.json \\
|
||||
--html ${prefix}.fastp.html \\
|
||||
$adapter_list \\
|
||||
$fail_fastq \\
|
||||
$args \\
|
||||
2> ${prefix}.fastp.log \\
|
||||
| gzip -c > ${prefix}.fastp.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else if (meta.single_end) {
|
||||
"""
|
||||
[ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
|
||||
|
||||
fastp \\
|
||||
--stdout \\
|
||||
--in1 ${prefix}.fastq.gz \\
|
||||
--out1 ${prefix}.fastp.fastq.gz \\
|
||||
--thread $task.cpus \\
|
||||
--json ${prefix}.fastp.json \\
|
||||
--html ${prefix}.fastp.html \\
|
||||
$adapter_list \\
|
||||
$fail_fastq \\
|
||||
$args \\
|
||||
2> ${prefix}.fastp.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
|
||||
"""
|
||||
[ ! -f ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
|
||||
[ ! -f ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
|
||||
fastp \\
|
||||
--in1 ${prefix}_1.fastq.gz \\
|
||||
--in2 ${prefix}_2.fastq.gz \\
|
||||
--out1 ${prefix}_1.fastp.fastq.gz \\
|
||||
--out2 ${prefix}_2.fastp.fastq.gz \\
|
||||
--json ${prefix}.fastp.json \\
|
||||
--html ${prefix}.fastp.html \\
|
||||
$adapter_list \\
|
||||
$fail_fastq \\
|
||||
$merge_fastq \\
|
||||
--thread $task.cpus \\
|
||||
--detect_adapter_for_pe \\
|
||||
$args \\
|
||||
2> ${prefix}.fastp.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,73 @@
|
||||
name: fastp
|
||||
description: Perform adapter/quality trimming on sequencing reads
|
||||
keywords:
|
||||
- trimming
|
||||
- quality control
|
||||
- fastq
|
||||
tools:
|
||||
- fastp:
|
||||
description: |
|
||||
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
|
||||
documentation: https://github.com/OpenGene/fastp
|
||||
doi: https://doi.org/10.1093/bioinformatics/bty560
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads.
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively. If you wish to run interleaved paired-end data, supply as single-end data
|
||||
but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.
|
||||
- adapter_fasta:
|
||||
type: file
|
||||
description: File in FASTA format containing possible adapters to remove.
|
||||
pattern: "*.{fasta,fna,fas,fa}"
|
||||
- save_trimmed_fail:
|
||||
type: boolean
|
||||
description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
|
||||
- save_merged:
|
||||
type: boolean
|
||||
description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: The trimmed/modified/unmerged fastq reads
|
||||
pattern: "*fastp.fastq.gz"
|
||||
- json:
|
||||
type: file
|
||||
description: Results in JSON format
|
||||
pattern: "*.json"
|
||||
- html:
|
||||
type: file
|
||||
description: Results in HTML format
|
||||
pattern: "*.html"
|
||||
- log:
|
||||
type: file
|
||||
description: fastq log file
|
||||
pattern: "*.log"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- reads_fail:
|
||||
type: file
|
||||
description: Reads the failed the preprocessing
|
||||
pattern: "*fail.fastq.gz"
|
||||
- reads_merged:
|
||||
type: file
|
||||
description: Reads that were successfully merged
|
||||
pattern: "*.{merged.fastq.gz}"
|
||||
authors:
|
||||
- "@drpatelh"
|
||||
- "@kevinmenden"
|
||||
@ -0,0 +1,39 @@
|
||||
process FILTLONG {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda "bioconda::filtlong=0.2.1"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
|
||||
'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(shortreads), path(longreads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fastq.gz"), emit: reads
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
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 short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
|
||||
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
|
||||
"""
|
||||
filtlong \\
|
||||
$short_reads \\
|
||||
$args \\
|
||||
$longreads \\
|
||||
2> ${prefix}.log \\
|
||||
| gzip -n > ${prefix}.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
filtlong: \$( filtlong --version | sed -e "s/Filtlong v//g" )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,55 @@
|
||||
name: filtlong
|
||||
description: Filtlong filters long reads based on quality measures or short read data.
|
||||
keywords:
|
||||
- nanopore
|
||||
- quality control
|
||||
- QC
|
||||
- filtering
|
||||
- long reads
|
||||
- short reads
|
||||
tools:
|
||||
- filtlong:
|
||||
description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
|
||||
homepage: https://anaconda.org/bioconda/filtlong
|
||||
documentation: None
|
||||
tool_dev_url: https://github.com/rrwick/Filtlong
|
||||
doi: ""
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- shortreads:
|
||||
type: file
|
||||
description: fastq file
|
||||
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
|
||||
- longreads:
|
||||
type: file
|
||||
description: fastq file
|
||||
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
|
||||
|
||||
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: Filtered (compressed) fastq file
|
||||
pattern: "*.fastq.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: Standard error logging file containing summary statistics
|
||||
pattern: "*.log"
|
||||
|
||||
authors:
|
||||
- "@d4straub"
|
||||
- "@sofstam"
|
||||
@ -0,0 +1,44 @@
|
||||
process GUNZIP {
|
||||
tag "$archive"
|
||||
label 'process_single'
|
||||
|
||||
conda "conda-forge::sed=4.7"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
|
||||
'ubuntu:20.04' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(archive)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("$gunzip"), emit: gunzip
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
gunzip = archive.toString() - '.gz'
|
||||
"""
|
||||
gunzip \\
|
||||
-f \\
|
||||
$args \\
|
||||
$archive
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
stub:
|
||||
gunzip = archive.toString() - '.gz'
|
||||
"""
|
||||
touch $gunzip
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,34 @@
|
||||
name: gunzip
|
||||
description: Compresses and decompresses files.
|
||||
keywords:
|
||||
- gunzip
|
||||
- compression
|
||||
tools:
|
||||
- gunzip:
|
||||
description: |
|
||||
gzip is a file format and a software application used for file compression and decompression.
|
||||
documentation: https://www.gnu.org/software/gzip/manual/gzip.html
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Optional groovy Map containing meta information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- archive:
|
||||
type: file
|
||||
description: File to be compressed/uncompressed
|
||||
pattern: "*.*"
|
||||
output:
|
||||
- gunzip:
|
||||
type: file
|
||||
description: Compressed/uncompressed file
|
||||
pattern: "*.*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,41 @@
|
||||
process KAIJU_KAIJU {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda "bioconda::kaiju=1.8.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
|
||||
'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path(db)
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.tsv'), emit: results
|
||||
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 = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
|
||||
"""
|
||||
dbnodes=`find -L ${db} -name "*nodes.dmp"`
|
||||
dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
|
||||
kaiju \\
|
||||
$args \\
|
||||
-z $task.cpus \\
|
||||
-t \$dbnodes \\
|
||||
-f \$dbname \\
|
||||
-o ${prefix}.tsv \\
|
||||
$input
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,53 @@
|
||||
name: kaiju_kaiju
|
||||
description: Taxonomic classification of metagenomic sequence data using a protein reference database
|
||||
keywords:
|
||||
- classify
|
||||
- metagenomics
|
||||
- fastq
|
||||
- taxonomic profiling
|
||||
tools:
|
||||
- kaiju:
|
||||
description: Fast and sensitive taxonomic classification for metagenomics
|
||||
homepage: https://kaiju.binf.ku.dk/
|
||||
documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
|
||||
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
|
||||
doi: "10.1038/ncomms11257"
|
||||
licence: ["GNU GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}"
|
||||
- db:
|
||||
type: files
|
||||
description: |
|
||||
List containing the database and nodes files for Kaiju
|
||||
e.g. [ 'database.fmi', 'nodes.dmp' ]
|
||||
|
||||
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"
|
||||
- results:
|
||||
type: file
|
||||
description: Results with taxonomic classification of each read
|
||||
pattern: "*.tsv"
|
||||
|
||||
authors:
|
||||
- "@talnor"
|
||||
- "@sofstam"
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,39 @@
|
||||
process KAIJU_KAIJU2KRONA {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::kaiju=1.8.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
|
||||
'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(tsv)
|
||||
path(db)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: txt
|
||||
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}"
|
||||
"""
|
||||
dbnodes=`find -L ${db} -name "*nodes.dmp"`
|
||||
dbnames=`find -L ${db} -name "*names.dmp"`
|
||||
kaiju2krona \\
|
||||
$args \\
|
||||
-t \$dbnodes \\
|
||||
-n \$dbnames \\
|
||||
-i ${tsv} \\
|
||||
-o ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,44 @@
|
||||
name: kaiju_kaiju2krona
|
||||
description: Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona.
|
||||
keywords:
|
||||
- taxonomy
|
||||
- visualisation
|
||||
- krona chart
|
||||
- metagenomics
|
||||
tools:
|
||||
- "kaiju":
|
||||
description: Fast and sensitive taxonomic classification for metagenomics
|
||||
homepage: https://kaiju.binf.ku.dk/
|
||||
documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
|
||||
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
|
||||
doi: "10.1038/ncomms11257"
|
||||
licence: ["GNU GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- tsv:
|
||||
type: file
|
||||
description: Kaiju tab-separated output file
|
||||
pattern: "*.{tsv,txt}"
|
||||
|
||||
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"
|
||||
- txt:
|
||||
type: file
|
||||
description: Krona text-based input file converted from Kaiju report
|
||||
pattern: "*.{txt,krona}"
|
||||
|
||||
authors:
|
||||
- "@MillironX"
|
||||
@ -0,0 +1,40 @@
|
||||
process KAIJU_KAIJU2TABLE {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::kaiju=1.8.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
|
||||
'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(results)
|
||||
path db
|
||||
val taxon_rank
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.txt'), emit: summary
|
||||
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}"
|
||||
"""
|
||||
dbnodes=`find -L ${db} -name "*nodes.dmp"`
|
||||
dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
|
||||
kaiju2table $args \\
|
||||
-t \$dbnodes \\
|
||||
-n \$dbname \\
|
||||
-r ${taxon_rank} \\
|
||||
-o ${prefix}.txt \\
|
||||
${results}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,50 @@
|
||||
name: "kaiju_kaiju2table"
|
||||
description: write your description here
|
||||
keywords:
|
||||
- classify
|
||||
- metagenomics
|
||||
tools:
|
||||
- kaiju:
|
||||
description: Fast and sensitive taxonomic classification for metagenomics
|
||||
homepage: https://kaiju.binf.ku.dk/
|
||||
documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
|
||||
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
|
||||
doi: "10.1038/ncomms11257"
|
||||
licence: ["GNU GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- results:
|
||||
type: file
|
||||
description: File containing the kaiju classification results
|
||||
pattern: "*.{txt}"
|
||||
- taxon_rank:
|
||||
type: string
|
||||
description: |
|
||||
Taxonomic rank to display in report
|
||||
pattern: "phylum|class|order|family|genus|species"
|
||||
|
||||
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"
|
||||
- results:
|
||||
type: file
|
||||
description: |
|
||||
Summary table for a given taxonomic rank
|
||||
pattern: "*.{tsv}"
|
||||
|
||||
authors:
|
||||
- "@sofstam"
|
||||
- "@talnor"
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,58 @@
|
||||
process KRAKEN2_KRAKEN2 {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda "bioconda::kraken2=2.1.2 conda-forge::pigz=2.6"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
|
||||
'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path db
|
||||
val save_output_fastqs
|
||||
val save_reads_assignment
|
||||
|
||||
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('*classifiedreads.txt') , optional:true, emit: classified_reads_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 prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def paired = meta.single_end ? "" : "--paired"
|
||||
def classified = meta.single_end ? "${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 readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null"
|
||||
def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
|
||||
|
||||
"""
|
||||
kraken2 \\
|
||||
--db $db \\
|
||||
--threads $task.cpus \\
|
||||
--report ${prefix}.kraken2.report.txt \\
|
||||
--gzip-compressed \\
|
||||
$unclassified_option \\
|
||||
$classified_option \\
|
||||
$readclassification_option \\
|
||||
$paired \\
|
||||
$args \\
|
||||
$reads
|
||||
|
||||
$compress_reads_command
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
|
||||
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,75 @@
|
||||
name: kraken2_kraken2
|
||||
description: Classifies metagenomic sequence data
|
||||
keywords:
|
||||
- classify
|
||||
- metagenomics
|
||||
- fastq
|
||||
- db
|
||||
tools:
|
||||
- kraken2:
|
||||
description: |
|
||||
Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
|
||||
homepage: https://ccb.jhu.edu/software/kraken2/
|
||||
documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
|
||||
doi: 10.1186/s13059-019-1891-0
|
||||
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 FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- db:
|
||||
type: directory
|
||||
description: Kraken2 database
|
||||
- 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 Kraken2 database.
|
||||
pattern: "*{fastq.gz}"
|
||||
- unclassified_reads_fastq:
|
||||
type: file
|
||||
description: |
|
||||
Reads not classified to any of the taxa
|
||||
on the Kraken2 database.
|
||||
pattern: "*{fastq.gz}"
|
||||
- classified_reads_assignment:
|
||||
type: file
|
||||
description: |
|
||||
Kraken2 output file indicating the taxonomic assignment of
|
||||
each input read
|
||||
- report:
|
||||
type: file
|
||||
description: |
|
||||
Kraken2 report containing stats about classified
|
||||
and not classifed reads.
|
||||
pattern: "*.{report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
@ -0,0 +1,34 @@
|
||||
process KRAKENTOOLS_COMBINEKREPORTS {
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::krakentools=1.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
|
||||
'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(kreports)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: txt
|
||||
path "versions.yml", emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
||||
"""
|
||||
combine_kreports.py \\
|
||||
-r ${kreports} \\
|
||||
-o ${prefix}.txt \\
|
||||
${args}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
combine_kreports.py: ${VERSION}
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,43 @@
|
||||
name: krakentools_combinekreports
|
||||
description: Takes a Kraken report file and prints out a krona-compatible TEXT file
|
||||
keywords:
|
||||
- kraken
|
||||
- krakentools
|
||||
- metagenomics
|
||||
- table
|
||||
- combining
|
||||
- merging
|
||||
tools:
|
||||
- krakentools:
|
||||
description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
|
||||
homepage: https://github.com/jenniferlu717/KrakenTools
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- kreports:
|
||||
type: file
|
||||
description: List of kraken-style report files
|
||||
pattern: "*.{txt,kreport}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- txt:
|
||||
type: file
|
||||
description: Combined kreport file of all input files
|
||||
pattern: "*.txt"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,36 @@
|
||||
process KRAKENTOOLS_KREPORT2KRONA {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
||||
conda "bioconda::krakentools=1.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
|
||||
'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(kreport)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: txt
|
||||
path "versions.yml", emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
||||
"""
|
||||
kreport2krona.py \\
|
||||
-r ${kreport} \\
|
||||
-o ${prefix}.txt \\
|
||||
${args}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
kreport2krona.py: ${VERSION}
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,41 @@
|
||||
name: krakentools_kreport2krona
|
||||
description: Takes a Kraken report file and prints out a krona-compatible TEXT file
|
||||
keywords:
|
||||
- kraken
|
||||
- krona
|
||||
- metagenomics
|
||||
- visualization
|
||||
tools:
|
||||
- krakentools:
|
||||
description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
|
||||
homepage: https://github.com/jenniferlu717/KrakenTools
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- kreport:
|
||||
type: file
|
||||
description: Kraken report
|
||||
pattern: "*.{txt,kreport}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- krona:
|
||||
type: file
|
||||
description: Krona text-based input file converted from Kraken report
|
||||
pattern: "*.{txt,krona}"
|
||||
|
||||
authors:
|
||||
- "@MillironX"
|
||||
@ -0,0 +1,224 @@
|
||||
process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda "bioconda::krakenuniq=1.0.2"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.2--pl5321h19e8d03_0':
|
||||
'quay.io/biocontainers/krakenuniq:1.0.2--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 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' : ''
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
krakenuniq \\
|
||||
--db $db \\
|
||||
--preload \\
|
||||
--preload-size $ram_chunk_size \\
|
||||
--threads $task.cpus \\
|
||||
$args
|
||||
|
||||
strip_suffix() {
|
||||
local result=\$1
|
||||
# Strip any file extensions.
|
||||
echo "\${result%%.*}"
|
||||
}
|
||||
|
||||
printf "%s\\n" ${fastqs} | while read FASTQ; do \\
|
||||
PREFIX="\$(strip_suffix "\${FASTQ}")"
|
||||
|
||||
krakenuniq \\
|
||||
--db $db \\
|
||||
--threads $task.cpus \\
|
||||
$report \\
|
||||
$output_option \\
|
||||
$unclassified_option \\
|
||||
$classified_option \\
|
||||
$output_option \\
|
||||
$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
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
krakenuniq \\
|
||||
--db $db \\
|
||||
--preload \\
|
||||
--preload-size $ram_chunk_size \\
|
||||
--threads $task.cpus \\
|
||||
$args
|
||||
|
||||
strip_suffix() {
|
||||
local result
|
||||
read result
|
||||
# Strip any trailing dot or underscore.
|
||||
result="\${result%_}"
|
||||
echo "\${result%.}"
|
||||
}
|
||||
|
||||
printf "%s %s\\n" ${fastqs} | while read FASTQ; do \\
|
||||
read -r -a FASTQ <<< "\${FASTQ}"
|
||||
PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
|
||||
|
||||
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 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' : ''
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
echo krakenuniq \\
|
||||
--db $db \\
|
||||
--preload \\
|
||||
--preload-size $ram_chunk_size \\
|
||||
--threads $task.cpus \\
|
||||
$args
|
||||
|
||||
strip_suffix() {
|
||||
local result=\$1
|
||||
# Strip any file extensions.
|
||||
echo "\${result%%.*}"
|
||||
}
|
||||
|
||||
printf "%s\\n" ${fastqs} | while read FASTQ; do \\
|
||||
echo "\${FASTQ}"
|
||||
PREFIX="\$(strip_suffix "\${FASTQ}")"
|
||||
echo "\${PREFIX}"
|
||||
|
||||
echo krakenuniq \\
|
||||
--db $db \\
|
||||
--threads $task.cpus \\
|
||||
$report \\
|
||||
$output_option \\
|
||||
$unclassified_option \\
|
||||
$classified_option \\
|
||||
$output_option \\
|
||||
$args2 \\
|
||||
"\${FASTQ}"
|
||||
|
||||
touch "\${PREFIX}.classified.fastq.gz"
|
||||
touch "\${PREFIX}.krakenuniq.classified.txt"
|
||||
touch "\${PREFIX}.krakenuniq.report.txt"
|
||||
touch "\${PREFIX}.unclassified.fastq.gz"
|
||||
done
|
||||
|
||||
echo $compress_reads_command
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
echo krakenuniq \\
|
||||
--db $db \\
|
||||
--preload \\
|
||||
--preload-size $ram_chunk_size \\
|
||||
--threads $task.cpus \\
|
||||
$args
|
||||
|
||||
strip_suffix() {
|
||||
local result
|
||||
read result
|
||||
# Strip any trailing dot or underscore.
|
||||
result="\${result%_}"
|
||||
echo "\${result%.}"
|
||||
}
|
||||
|
||||
printf "%s %s\\n" ${fastqs} | while read FASTQ; do \\
|
||||
read -r -a FASTQ <<< "\${FASTQ}"
|
||||
echo "\${FASTQ[@]}"
|
||||
PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
|
||||
echo "\${PREFIX}"
|
||||
|
||||
echo krakenuniq \\
|
||||
--db $db \\
|
||||
--threads $task.cpus \\
|
||||
$report \\
|
||||
$output_option \\
|
||||
$unclassified_option \\
|
||||
$classified_option \\
|
||||
$output_option \\
|
||||
--paired \\
|
||||
$args2 \\
|
||||
"\${FASTQ[@]}"
|
||||
|
||||
touch "\${PREFIX}.classified_1.fastq.gz" "\${PREFIX}.classified_2.fastq.gz"
|
||||
touch "\${PREFIX}.krakenuniq.classified.txt"
|
||||
touch "\${PREFIX}.krakenuniq.report.txt"
|
||||
touch "\${PREFIX}.unclassified_1.fastq.gz" "\${PREFIX}.unclassified_2.fastq.gz"
|
||||
done
|
||||
|
||||
echo $compress_reads_command
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,78 @@
|
||||
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"
|
||||
- "@Midnighter"
|
||||
@ -0,0 +1,41 @@
|
||||
process KRONA_KTIMPORTTAXONOMY {
|
||||
tag "${meta.id}"
|
||||
label 'process_single'
|
||||
|
||||
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
||||
conda "bioconda::krona=2.8"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
|
||||
'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
path taxonomy, stageAs: 'taxonomy.tab'
|
||||
|
||||
output:
|
||||
tuple val(meta), path ('*.html'), emit: html
|
||||
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 VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
||||
"""
|
||||
TAXONOMY=\$(find -L . -name '*.tab' -exec dirname {} \\;)
|
||||
echo \$TAXONOMY
|
||||
|
||||
ktImportTaxonomy \\
|
||||
$args \\
|
||||
-o ${prefix}.html \\
|
||||
-tax \$TAXONOMY/ \\
|
||||
$report
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
krona: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,48 @@
|
||||
name: krona_ktimporttaxonomy
|
||||
description: KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.
|
||||
keywords:
|
||||
- plot
|
||||
- taxonomy
|
||||
- interactive
|
||||
- html
|
||||
- visualisation
|
||||
- krona chart
|
||||
tools:
|
||||
- krona:
|
||||
description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
|
||||
homepage: https://github.com/marbl/Krona/wiki/KronaTools
|
||||
documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
|
||||
tool_dev_url:
|
||||
doi: https://doi.org/10.1186/1471-2105-12-385
|
||||
licence:
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test']
|
||||
- database:
|
||||
type: file
|
||||
description: |
|
||||
Path to a Krona taxonomy .tab file normally downloaded and generated by
|
||||
krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but
|
||||
must end in `.tab`.
|
||||
pattern: "*tab"
|
||||
- report:
|
||||
type: file
|
||||
description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored."
|
||||
pattern: "*.{tsv}"
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- html:
|
||||
type: file
|
||||
description: A html file containing an interactive krona plot.
|
||||
pattern: "*.{html}"
|
||||
|
||||
authors:
|
||||
- "@mjakobs"
|
||||
@ -0,0 +1,34 @@
|
||||
process KRONA_KTIMPORTTEXT {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::krona=2.8.1"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
|
||||
'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
|
||||
output:
|
||||
tuple val(meta), path ('*.html'), emit: html
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
ktImportText \\
|
||||
$args \\
|
||||
-o ${prefix}.html \\
|
||||
$report
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,47 @@
|
||||
name: "krona_ktimporttext"
|
||||
description: Creates a Krona chart from text files listing quantities and lineages.
|
||||
keywords:
|
||||
- plot
|
||||
- taxonomy
|
||||
- interactive
|
||||
- html
|
||||
- visualisation
|
||||
- krona chart
|
||||
- metagenomics
|
||||
tools:
|
||||
- krona:
|
||||
description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
|
||||
homepage: https://github.com/marbl/Krona/wiki/KronaTools
|
||||
documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
|
||||
tool_dev_url: https://github.com/marbl/Krona
|
||||
doi: 10.1186/1471-2105-12-385
|
||||
licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test']
|
||||
- report:
|
||||
type: file
|
||||
description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored."
|
||||
pattern: "*.{txt}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test' ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- html:
|
||||
type: file
|
||||
description: A html file containing an interactive krona plot.
|
||||
pattern: "*.{html}"
|
||||
|
||||
authors:
|
||||
- "@jianhong"
|
||||
@ -0,0 +1,47 @@
|
||||
process MALT_RUN {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda "bioconda::malt=0.61"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
|
||||
'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fastqs)
|
||||
path index
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.rma6") , emit: rma6
|
||||
tuple val(meta), path("*.{tab,text,sam}"), optional:true, emit: alignments
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
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 avail_mem = 6
|
||||
if (!task.memory) {
|
||||
log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
|
||||
"""
|
||||
malt-run \\
|
||||
-t $task.cpus \\
|
||||
-v \\
|
||||
-o . \\
|
||||
$args \\
|
||||
--inFile ${fastqs.join(' ')} \\
|
||||
--index $index/ |&tee ${prefix}-malt-run.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
malt: \$(malt-run --help 2>&1 | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,54 @@
|
||||
name: malt_run
|
||||
description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
|
||||
keywords:
|
||||
- malt
|
||||
- alignment
|
||||
- metagenomics
|
||||
- ancient DNA
|
||||
- aDNA
|
||||
- palaeogenomics
|
||||
- archaeogenomics
|
||||
- microbiome
|
||||
tools:
|
||||
- malt:
|
||||
description: A tool for mapping metagenomic data
|
||||
homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
|
||||
documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
|
||||
tool_dev_url: None
|
||||
doi: "10.1038/s41559-017-0446-6"
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fastqs:
|
||||
type: file
|
||||
description: Input FASTQ files
|
||||
pattern: "*.{fastq.gz,fq.gz}"
|
||||
- index:
|
||||
type: directory
|
||||
description: Index/database directory from malt-build
|
||||
pattern: "*/"
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- rma6:
|
||||
type: file
|
||||
description: MEGAN6 RMA6 file
|
||||
pattern: "*.rma6"
|
||||
- sam:
|
||||
type: file
|
||||
description: Alignment files in Tab, Text or MEGAN-compatible SAM format
|
||||
pattern: "*.{tab,txt,sam}"
|
||||
- log:
|
||||
type: file
|
||||
description: Log of verbose MALT stdout
|
||||
pattern: "*-malt-run.log"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,38 @@
|
||||
process MEGAN_RMA2INFO {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::megan=6.21.7"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
|
||||
'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(rma6)
|
||||
val(megan_summary)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt.gz") , emit: txt
|
||||
tuple val(meta), path("*.megan"), optional: true, emit: megan_summary
|
||||
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 summary = megan_summary ? "-es ${prefix}.megan" : ""
|
||||
"""
|
||||
rma2info \\
|
||||
-i ${rma6} \\
|
||||
-o ${prefix}.txt.gz \\
|
||||
${summary} \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
megan: \$(echo \$(rma2info 2>&1) | grep version | sed 's/.*version //g;s/, built.*//g')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,51 @@
|
||||
name: "megan_rma2info"
|
||||
description: Analyses an RMA file and exports information in text format
|
||||
keywords:
|
||||
- megan
|
||||
- rma6
|
||||
- classification
|
||||
- conversion
|
||||
tools:
|
||||
- "megan":
|
||||
description: "A tool for studying the taxonomic content of a set of DNA reads"
|
||||
homepage: "https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/megan6/"
|
||||
documentation: "https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html"
|
||||
tool_dev_url: "https://github.com/husonlab/megan-ce"
|
||||
doi: "10.1371/journal.pcbi.1004957"
|
||||
licence: "['GPL >=3']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- rma6:
|
||||
type: file
|
||||
description: RMA6 file from MEGAN or MALT
|
||||
pattern: "*.rma6"
|
||||
- megan_summary:
|
||||
type: boolean
|
||||
description: Specify whether to generate an MEGAN summary file
|
||||
|
||||
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"
|
||||
- txt:
|
||||
type: file
|
||||
description: Compressed text file
|
||||
pattern: "*.txt.gz"
|
||||
- megan_summary:
|
||||
type: file
|
||||
description: Optionally generated MEGAN summary file
|
||||
pattern: "*.megan"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,33 @@
|
||||
process METAPHLAN3_MERGEMETAPHLANTABLES {
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::metaphlan=3.0.12"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
|
||||
'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(profiles)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.txt") , emit: txt
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
merge_metaphlan_tables.py \\
|
||||
$args \\
|
||||
-o ${prefix}.txt \\
|
||||
${profiles}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,44 @@
|
||||
name: "metaphlan3_mergemetaphlantables"
|
||||
description: Merges output abundance tables from MetaPhlAn3
|
||||
keywords:
|
||||
- metagenomics
|
||||
- classification
|
||||
- merge
|
||||
- table
|
||||
- profiles
|
||||
tools:
|
||||
- metaphlan3:
|
||||
description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
|
||||
homepage: https://huttenhower.sph.harvard.edu/metaphlan/
|
||||
documentation: https://github.com/biobakery/MetaPhlAn
|
||||
doi: "10.7554/eLife.65088"
|
||||
licence: ["MIT License"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- profiles:
|
||||
type: file
|
||||
description: List of per-sample MetaPhlAn3 taxonomic abundance tables
|
||||
pattern: "*"
|
||||
|
||||
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"
|
||||
- txt:
|
||||
type: txt
|
||||
description: Combined MetaPhlAn3 table
|
||||
pattern: "*.txt"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,48 @@
|
||||
process METAPHLAN3_METAPHLAN3 {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda "bioconda::metaphlan=3.0.12"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
|
||||
'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
path metaphlan_db
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_profile.txt") , emit: profile
|
||||
tuple val(meta), path("*.biom") , emit: biom
|
||||
tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def input_type = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
|
||||
def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
|
||||
def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
|
||||
|
||||
"""
|
||||
BT2_DB=`find -L "${metaphlan_db}" -name "*rev.1.bt2" -exec dirname {} \\;`
|
||||
|
||||
metaphlan \\
|
||||
--nproc $task.cpus \\
|
||||
$input_type \\
|
||||
$input_data \\
|
||||
$args \\
|
||||
$bowtie2_out \\
|
||||
--bowtie2db \$BT2_DB \\
|
||||
--biom ${prefix}.biom \\
|
||||
--output_file ${prefix}_profile.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,58 @@
|
||||
name: metaphlan3_metaphlan3
|
||||
description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
|
||||
keywords:
|
||||
- metagenomics
|
||||
- classification
|
||||
- fastq
|
||||
- bam
|
||||
- fasta
|
||||
tools:
|
||||
- metaphlan3:
|
||||
description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
|
||||
homepage: https://huttenhower.sph.harvard.edu/metaphlan/
|
||||
documentation: https://github.com/biobakery/MetaPhlAn
|
||||
doi: "10.7554/eLife.65088"
|
||||
licence: ["MIT License"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- input:
|
||||
type: file
|
||||
description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)
|
||||
pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}"
|
||||
- metaphlan_db:
|
||||
type: file
|
||||
description: |
|
||||
Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.
|
||||
Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!
|
||||
pattern: "*/"
|
||||
|
||||
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"
|
||||
- profile:
|
||||
type: file
|
||||
description: Tab-separated output file of the predicted taxon relative abundances
|
||||
pattern: "*.{txt}"
|
||||
- biom:
|
||||
type: file
|
||||
description: General-use format for representing biological sample by observation contingency tables
|
||||
pattern: "*.{biom}"
|
||||
- bowtie2out:
|
||||
type: file
|
||||
description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )
|
||||
pattern: "*.{bowtie2out.txt}"
|
||||
|
||||
authors:
|
||||
- "@MGordon09"
|
||||
@ -0,0 +1,48 @@
|
||||
process MINIMAP2_ALIGN {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
// Note: the versions here need to match the versions used in the mulled container below and minimap2/index
|
||||
conda "bioconda::minimap2=2.24 bioconda::samtools=1.14"
|
||||
container "${ 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)
|
||||
path reference
|
||||
val bam_format
|
||||
val cigar_paf_format
|
||||
val cigar_bam
|
||||
|
||||
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 bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
|
||||
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
|
||||
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
|
||||
"""
|
||||
minimap2 \\
|
||||
$args \\
|
||||
-t $task.cpus \\
|
||||
"${reference ?: reads}" \\
|
||||
"$reads" \\
|
||||
$cigar_paf \\
|
||||
$set_cigar_bam \\
|
||||
$bam_output
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
minimap2: \$(minimap2 --version 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -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"
|
||||
@ -0,0 +1,34 @@
|
||||
process MINIMAP2_INDEX {
|
||||
label 'process_medium'
|
||||
|
||||
// Note: the versions here need to match the versions used in minimap2/align
|
||||
conda "bioconda::minimap2=2.24"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/minimap2:2.24--h7132678_1' :
|
||||
'quay.io/biocontainers/minimap2:2.24--h7132678_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), 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
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,40 @@
|
||||
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:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: |
|
||||
Reference database in FASTA format.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- index:
|
||||
type: file
|
||||
description: Minimap2 fasta index.
|
||||
pattern: "*.mmi"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@yuukiiwa"
|
||||
- "@drpatelh"
|
||||
@ -0,0 +1,45 @@
|
||||
process MOTUS_MERGE {
|
||||
tag "$meta.id"
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::motus=3.0.3"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway
|
||||
path profile_version_yml, stageAs: 'profile_version.yml'
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt") , optional: true, emit: txt
|
||||
tuple val(meta), path("*.biom"), optional: true, emit: biom
|
||||
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 cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
|
||||
def suffix = task.ext.args?.contains("-B") ? "biom" : "txt"
|
||||
"""
|
||||
motus \\
|
||||
merge \\
|
||||
-db $db \\
|
||||
${cmd_input} \\
|
||||
$args \\
|
||||
-o ${prefix}.${suffix}
|
||||
|
||||
## Take version from the mOTUs/profile module output, as cannot reconstruct
|
||||
## version without having database staged in this directory.
|
||||
VERSION=\$(cat ${profile_version_yml} | grep '/*motus:.*' | sed 's/.*otus: //g')
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
motus: \$VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,54 @@
|
||||
name: "motus_merge"
|
||||
description: Taxonomic meta-omics profiling using universal marker genes
|
||||
keywords:
|
||||
- classify
|
||||
- metagenomics
|
||||
- fastq
|
||||
- taxonomic profiling
|
||||
- merging
|
||||
- merge
|
||||
- otu table
|
||||
tools:
|
||||
- "motus":
|
||||
description: "Marker gene-based OTU (mOTU) profiling"
|
||||
homepage: "https://motu-tool.org/"
|
||||
documentation: "https://github.com/motu-tool/mOTUs/wiki"
|
||||
tool_dev_url: "https://github.com/motu-tool/mOTUs"
|
||||
doi: "10.1186/s40168-022-01410-z"
|
||||
licence: "['GPL v3']"
|
||||
|
||||
input:
|
||||
- input:
|
||||
type: file
|
||||
description: |
|
||||
List of output files (more than one) from motus profile,
|
||||
or a single directory containing motus output files.
|
||||
- db:
|
||||
type: directory
|
||||
description: |
|
||||
mOTUs database downloaded by `motus downloadDB`
|
||||
pattern: "db_mOTU/"
|
||||
- profile_version_yml:
|
||||
type: file
|
||||
description: |
|
||||
A single versions.yml file output from motus/profile. motus/merge cannot reconstruct
|
||||
this itself without having the motus database present and configured with the tool
|
||||
so here we take it from what is already reported by the upstream module.
|
||||
pattern: "versions.yml"
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- txt:
|
||||
type: file
|
||||
description: OTU table in txt format, if BIOM format not requested
|
||||
pattern: "*.txt"
|
||||
- biom:
|
||||
type: file
|
||||
description: OTU table in biom format, if BIOM format requested
|
||||
pattern: "*.biom"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
@ -0,0 +1,56 @@
|
||||
process MOTUS_PROFILE {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda "bioconda::motus=3.0.3"
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path db
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.out"), emit: out
|
||||
tuple val(meta), path("*.bam"), optional: true, emit: bam
|
||||
tuple val(meta), path("*.mgc"), optional: true, emit: mgc
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
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 inputs = reads[0].getExtension() == 'bam' ?
|
||||
"-i ${reads}" :
|
||||
reads[0].getExtension() == 'mgc' ? "-m $reads" :
|
||||
meta.single_end ?
|
||||
"-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
|
||||
def refdb = db ? "-db ${db}" : ""
|
||||
"""
|
||||
motus profile \\
|
||||
$args \\
|
||||
$inputs \\
|
||||
$refdb \\
|
||||
-t $task.cpus \\
|
||||
-n $prefix \\
|
||||
-o ${prefix}.out \\
|
||||
2> ${prefix}.log
|
||||
|
||||
## mOTUs version number is not available from command line.
|
||||
## mOTUs save the version number in index database folder.
|
||||
## mOTUs will check the database version is same version as exec version.
|
||||
if [ "$db" == "" ]; then
|
||||
VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
|
||||
else
|
||||
VERSION=\$(grep motus $db/db_mOTU_versions | sed 's/motus\\t//g')
|
||||
fi
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
motus: \$VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
@ -0,0 +1,65 @@
|
||||
name: "motus_profile"
|
||||
description: Taxonomic meta-omics profiling using universal marker genes
|
||||
keywords:
|
||||
- classify
|
||||
- metagenomics
|
||||
- fastq
|
||||
- taxonomic profiling
|
||||
tools:
|
||||
- "motus":
|
||||
description: "Marker gene-based OTU (mOTU) profiling"
|
||||
homepage: "https://motu-tool.org/"
|
||||
documentation: "https://github.com/motu-tool/mOTUs/wiki"
|
||||
tool_dev_url: "https://github.com/motu-tool/mOTUs"
|
||||
doi: "10.1186/s40168-022-01410-z"
|
||||
licence: "['GPL v3']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
Or the intermediate bam file mapped by bwa to the mOTUs database or
|
||||
the output bam file from motus profile.
|
||||
Or the intermediate mgc read counts table.
|
||||
pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
|
||||
- db:
|
||||
type: directory
|
||||
description: |
|
||||
mOTUs database downloaded by `motus downloadDB`
|
||||
|
||||
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"
|
||||
- out:
|
||||
type: file
|
||||
description: Results with taxonomic classification of each read
|
||||
pattern: "*.out"
|
||||
- bam:
|
||||
type: file
|
||||
description: Optional intermediate sorted BAM file from BWA
|
||||
pattern: "*.{bam}"
|
||||
- mgc:
|
||||
type: file
|
||||
description: Optional intermediate mgc read count table file saved with `-M`.
|
||||
pattern: "*.{mgc}"
|
||||
- log:
|
||||
type: file
|
||||
description: Standard error logging file containing summary statistics
|
||||
pattern: "*.log"
|
||||
|
||||
authors:
|
||||
- "@jianhong"
|
||||
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Reference in New Issue