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https://github.com/MillironX/taxprofiler.git
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Add draft version of DIAMOND
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parent
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commit
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10 changed files with 216 additions and 27 deletions
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@ -52,6 +52,10 @@
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> Kim, Daehwan, Li Song, Florian P. Breitwieser, and Steven L. Salzberg. 2016. “Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.” Genome Research 26 (12): 1721-29. doi: 10.1101/gr.210641.116.
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- [DIAMOND](https://doi.org/10.1038/nmeth.3176)
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> Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.
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## Software packaging/containerisation tools
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- [Anaconda](https://anaconda.com)
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@ -264,6 +264,36 @@ process {
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]
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}
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withName: KAIJU_KAIJU {
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.tsv'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KAIJU_KAIJU2TABLE {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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withName: DIAMOND_BLASTX {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/diamond/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{blast,xml,txt,daa,sam,tsv,paf}'
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]
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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@ -279,24 +309,4 @@ process {
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: KAIJU_KAIJU {
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.tsv'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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}
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withName: KAIJU_KAIJU2TABLE {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt}'
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]
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}
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}
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@ -34,6 +34,11 @@ params {
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run_malt = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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// TODO: setting to txt here as does not require taxonomy in database.
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// Should consider re-building our test database but with the required
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// taxonomy files, but this may make large files (prot2access: 9GB)
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diamond_output_format = 'txt'
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}
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process {
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@ -128,6 +128,9 @@ Expected (uncompressed) database files for each tool are as follows:
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- `kaiju_db_*.fmi`
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- `nodes.dmp`
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- `names.dmp`
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- **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
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to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
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- `<database_name>.dmnd`
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## Running the pipeline
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@ -27,6 +27,9 @@
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"custom/dumpsoftwareversions": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"diamond/blastx": {
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"git_sha": "42564565b934eeb2449e35ec97ed13ff2a67f1de"
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},
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"fastp": {
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"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
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},
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@ -65,4 +68,4 @@
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}
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}
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}
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}
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}
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53
modules/nf-core/modules/diamond/blastx/main.nf
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53
modules/nf-core/modules/diamond/blastx/main.nf
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@ -0,0 +1,53 @@
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process DIAMOND_BLASTX {
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tag "$meta.id"
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label 'process_medium'
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// Dimaond is limited to v2.0.9 because there is not a
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// singularity version higher than this at the current time.
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conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
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'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
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input:
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tuple val(meta), path(fasta)
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path db
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val outext
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output:
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tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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switch ( outext ) {
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case "blast": outfmt = 0; break
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case "xml": outfmt = 5; break
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case "txt": outfmt = 6; break
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case "daa": outfmt = 100; break
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case "sam": outfmt = 101; break
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case "tsv": outfmt = 102; break
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case "paf": outfmt = 103; break
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}
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"""
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DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
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diamond \\
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blastx \\
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--threads $task.cpus \\
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--db \$DB \\
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--query $fasta \\
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--outfmt ${outfmt} \\
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$args \\
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--out ${prefix}.${outext}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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diamond: \$(diamond --version 2>&1 | tail -n 1 | sed 's/^diamond version //')
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END_VERSIONS
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"""
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}
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52
modules/nf-core/modules/diamond/blastx/meta.yml
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52
modules/nf-core/modules/diamond/blastx/meta.yml
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name: diamond_blastx
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description: Queries a DIAMOND database using blastx mode
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keywords:
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- fasta
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- diamond
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- blastx
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- DNA sequence
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tools:
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- diamond:
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description: Accelerated BLAST compatible local sequence aligner
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homepage: https://github.com/bbuchfink/diamond
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documentation: https://github.com/bbuchfink/diamond/wiki
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tool_dev_url: https://github.com/bbuchfink/diamond
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doi: "doi:10.1038/s41592-021-01101-x"
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licence: ["GPL v3.0"]
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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 query sequences
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pattern: "*.{fa,fasta}"
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- db:
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type: directory
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description: Directory containing the nucelotide blast database
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pattern: "*"
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- outext:
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type: string
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description: |
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Specify the type of output file to be generated. `blast` corresponds to
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BLAST pairwise format. `xml` corresponds to BLAST xml format.
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`txt` corresponds to to BLAST tabular format. `tsv` corresponds to
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taxonomic classification format.
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pattern: "blast|xml|txt|daa|sam|tsv|paf"
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output:
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- txt:
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type: file
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description: File containing blastx hits
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pattern: "*.{blastx.txt}"
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- versions:
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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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- "@spficklin"
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- "@jfy133"
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@ -108,6 +108,10 @@ params {
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// kaiju
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run_kaiju = false
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kaiju_taxon_name = 'species'
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// diamond
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run_diamond = false
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diamond_output_format = 'tsv'
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}
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// Load base.config by default for all pipelines
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"hidden": true
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},
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"email_on_fail": {
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"]
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"enum": [
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"fastp",
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"adapterremoval"
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]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"]
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"enum": [
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"entropy",
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"dust"
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]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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"kaiju_taxon_name": {
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"type": "string",
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"default": "species",
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"enum": ["phylum", "class", "order", "family", "genus", "species"]
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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]
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},
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"run_diamond": {
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"type": "boolean"
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},
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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]
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}
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}
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}
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}
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@ -10,6 +10,8 @@ include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/cent
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include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
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include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
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include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
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include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main'
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workflow PROFILING {
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take:
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metaphlan3: it[2]['tool'] == 'metaphlan3'
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centrifuge: it[2]['tool'] == 'centrifuge'
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kaiju: it[2]['tool'] == 'kaiju'
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diamond: it[2]['tool'] == 'diamond'
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unknown: true
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}
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db: it[3]
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}
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ch_input_for_diamond = ch_input_for_profiling.diamond
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.multiMap {
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it ->
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reads: [it[0] + it[2], it[1]]
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db: it[3]
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}
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/*
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RUN PROFILING
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*/
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ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
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}
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if ( params.run_diamond ) {
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DIAMOND_BLASTX ( ch_input_for_diamond.reads, ch_input_for_diamond.db, params.diamond_output_format )
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ch_versions = ch_versions.mix( DIAMOND_BLASTX.out.versions.first() )
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ch_raw_profiles = ch_raw_profiles.mix( DIAMOND_BLASTX.out.output )
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}
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emit:
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profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom
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versions = ch_versions // channel: [ versions.yml ]
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