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Merge pull request #84 from EBI-Metagenomics/assembly_decontamination
Assembly decontamination subworkflow
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‎.prettierignore

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@@ -16,3 +16,4 @@ __pycache__
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*.pyc
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.github/renovate.json5
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*.pac
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*.njs

‎README.md

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@@ -46,6 +46,10 @@ Then import the desired module in your pipeline script:
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include { <subworkflow_name> } from '../subworkflows/ebi-metagenomics/<subworkflow_name>.nf'
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```
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## nf-core modules
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The [nf-core](https://nf-co.re/) team supports a large number of high-quality modules, and our team contributes whenever we can. At the moment, the [nf-core tools](https://github.com/nf-core/tools/) don't support subworkflows that install modules from different repos ([#3083](https://github.com/nf-core/tools/pull/3083)). That is why we decided to copy some modules from nf-core into this repo (a nasty hack, but it works). The nf-core team has been making impressive progress on supporting this use case (subworkflows with modules from different repos), and we will remove the duplicated modules once they reach that point. In the meantime, you will find duplicated modules from nf-core here.
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## References
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This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).

‎modules/ebi-metagenomics/blast/blastn/environment.yml

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::blast=2.15.0

‎modules/ebi-metagenomics/blast/blastn/main.nf

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process BLAST_BLASTN {
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tag "$meta.id"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1':
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'biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
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input:
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tuple val(meta) , path(fasta)
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tuple val(meta2), path(db)
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output:
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tuple val(meta), path('*.txt'), emit: txt
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def is_compressed = fasta.getExtension() == "gz" ? true : false
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def fasta_name = is_compressed ? fasta.getBaseName() : fasta
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"""
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if [ "${is_compressed}" == "true" ]; then
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gzip -c -d ${fasta} > ${fasta_name}
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fi
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DB=`find -L ./ -name "*.nal" | sed 's/\\.nal\$//'`
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if [ -z "\$DB" ]; then
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DB=`find -L ./ -name "*.nin" | sed 's/\\.nin\$//'`
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fi
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echo Using \$DB
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blastn \\
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-num_threads ${task.cpus} \\
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-db \$DB \\
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-query ${fasta_name} \\
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${args} \\
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-out ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
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END_VERSIONS
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"""
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}

‎modules/ebi-metagenomics/blast/blastn/meta.yml

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name: blast_blastn
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description: Queries a BLAST DNA database
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keywords:
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- fasta
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- blast
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- blastn
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- DNA sequence
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tools:
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- blast:
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description: |
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BLAST finds regions of similarity between biological sequences.
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homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
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documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
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doi: 10.1016/S0022-2836(05)80360-2
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licence: ["US-Government-Work"]
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identifier: ""
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: Input fasta file containing queries sequences
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pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
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- - meta2:
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type: map
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description: |
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Groovy Map containing db information
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e.g. [ id:'test2', single_end:false ]
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- db:
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type: directory
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description: Directory containing the blast database
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pattern: "*"
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output:
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- txt:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- "*.txt":
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type: file
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description: File containing blastn hits
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pattern: "*.txt"
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- versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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maintainers:
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- "@joseespinosa"
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- "@drpatelh"
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- "@vagkaratzas"

‎modules/ebi-metagenomics/blast/blastn/tests/main.nf.test

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nextflow_process {
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name "Test Process BLAST_BLASTN"
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script "../main.nf"
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process "BLAST_BLASTN"
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config "./nextflow.config"
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tag "modules"
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tag "modules_nfcore"
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tag "modules_ebimetagenomics"
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tag "blast"
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tag "blast/blastn"
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tag "blast/makeblastdb"
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setup {
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run("BLAST_MAKEBLASTDB") {
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script "../../makeblastdb/main.nf"
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process {
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"""
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input[0] = [ [id:'test2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
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"""
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}
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}
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}
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test("Should search for nucleotide hits against a blast db") {
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when {
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params {
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outdir = "$outputDir"
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}
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process {
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"""
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input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
34+
input[1] = BLAST_MAKEBLASTDB.out.db
35+
"""
36+
}
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}
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39+
then {
40+
assertAll(
41+
{ assert process.success },
42+
{ assert path(process.out.txt[0][1]).getText().contains("Query= MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate") },
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{ assert snapshot(process.out.versions).match("versions") }
44+
)
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}
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47+
}
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49+
test("Should search for zipped nucleotide hits against a blast db") {
50+
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when {
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params {
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outdir = "$outputDir"
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}
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process {
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"""
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input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) ]
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input[1] = BLAST_MAKEBLASTDB.out.db
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"""
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}
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}
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then {
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assertAll(
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{ assert process.success },
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{ assert path(process.out.txt[0][1]).getText().contains("Query= MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate") },
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{ assert snapshot(process.out.versions).match("versions_zipped") }
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)
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}
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}
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}

‎modules/ebi-metagenomics/blast/blastn/tests/main.nf.test.snap

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{
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"versions": {
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"content": [
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[
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"versions.yml:md5,faf2471d836ebbf24d96d3e1f8720b17"
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]
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],
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"timestamp": "2023-12-11T07:20:03.54997013"
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},
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"versions_zipped": {
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"content": [
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[
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"versions.yml:md5,faf2471d836ebbf24d96d3e1f8720b17"
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]
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],
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"timestamp": "2023-12-11T07:20:12.925782708"
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}
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}

‎modules/ebi-metagenomics/blast/blastn/tests/nextflow.config

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process {
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withName: BLAST_MAKEBLASTDB {
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ext.args = '-dbtype nucl'
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}
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}

‎modules/ebi-metagenomics/blast/blastn/tests/tags.yml

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blast/blastn:
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- modules/nf-core/blast/blastn/**

‎modules/ebi-metagenomics/blast/makeblastdb/environment.yml

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::blast=2.15.0

‎modules/ebi-metagenomics/blast/makeblastdb/main.nf

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@@ -1,30 +1,62 @@
11
process BLAST_MAKEBLASTDB {
2-
tag "$fasta"
2+
tag "$meta.id"
33
label 'process_medium'
44

5-
conda "bioconda::blast=2.13.0"
5+
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
8-
'biocontainers/blast:2.13.0--hf3cf87c_0' }"
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'https://depot.galaxyproject.org/singularity/blast:2.15.0--pl5321h6f7f691_1':
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'biocontainers/blast:2.15.0--pl5321h6f7f691_1' }"
99

1010
input:
11-
path fasta
11+
tuple val(meta), path(fasta)
1212

1313
output:
14-
path 'blast_db' , emit: db
15-
path "versions.yml" , emit: versions
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tuple val(meta), path("${meta.id}"), emit: db
15+
path "versions.yml" , emit: versions
1616

1717
when:
1818
task.ext.when == null || task.ext.when
1919

2020
script:
2121
def args = task.ext.args ?: ''
22+
def prefix = task.ext.prefix ?: "${meta.id}"
23+
def is_compressed = fasta.getExtension() == "gz" ? true : false
24+
def fasta_name = is_compressed ? fasta.getBaseName() : fasta
2225
"""
26+
if [ "${is_compressed}" == "true" ]; then
27+
gzip -c -d ${fasta} > ${fasta_name}
28+
fi
29+
2330
makeblastdb \\
24-
-in $fasta \\
25-
$args
26-
mkdir blast_db
27-
mv ${fasta}* blast_db
31+
-in ${fasta_name} \\
32+
${args}
33+
mkdir ${prefix}
34+
mv ${fasta_name}* ${prefix}
35+
36+
cat <<-END_VERSIONS > versions.yml
37+
"${task.process}":
38+
blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
39+
END_VERSIONS
40+
"""
41+
42+
stub:
43+
def args = task.ext.args ?: ''
44+
def prefix = task.ext.prefix ?: "${meta.id}"
45+
def is_compressed = fasta.getExtension() == "gz" ? true : false
46+
def fasta_name = is_compressed ? fasta.getBaseName() : fasta
47+
"""
48+
touch ${fasta_name}.fasta
49+
touch ${fasta_name}.fasta.ndb
50+
touch ${fasta_name}.fasta.nhr
51+
touch ${fasta_name}.fasta.nin
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touch ${fasta_name}.fasta.njs
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touch ${fasta_name}.fasta.not
54+
touch ${fasta_name}.fasta.nsq
55+
touch ${fasta_name}.fasta.ntf
56+
touch ${fasta_name}.fasta.nto
57+
mkdir ${prefix}
58+
mv ${fasta_name}* ${prefix}
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2860
cat <<-END_VERSIONS > versions.yml
2961
"${task.process}":
3062
blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')

‎modules/ebi-metagenomics/blast/makeblastdb/meta.yml

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documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
1313
doi: 10.1016/S0022-2836(05)80360-2
1414
licence: ["US-Government-Work"]
15+
identifier: ""
1516
input:
16-
- fasta:
17-
type: file
18-
description: Input fasta file
19-
pattern: "*.{fa,fasta}"
17+
- - meta:
18+
type: map
19+
description: |
20+
Groovy Map containing sample information
21+
e.g. [ id:'test', single_end:false ]
22+
- fasta:
23+
type: file
24+
description: Input fasta file
25+
pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
2026
output:
2127
- db:
22-
type: directory
23-
description: Output directory containing blast database files
24-
pattern: "*"
28+
- meta:
29+
type: map
30+
description: |
31+
Groovy Map containing sample information
32+
e.g. [ id:'test', single_end:false ]
33+
- ${meta.id}:
34+
type: directory
35+
description: Output directory containing blast database files
36+
pattern: "*"
2537
- versions:
26-
type: file
27-
description: File containing software versions
28-
pattern: "versions.yml"
38+
- versions.yml:
39+
type: file
40+
description: File containing software versions
41+
pattern: "versions.yml"
2942
authors:
3043
- "@joseespinosa"
3144
- "@drpatelh"
45+
maintainers:
46+
- "@joseespinosa"
47+
- "@drpatelh"
48+
- "@vagkaratzas"

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