diff --git a/CITATIONS.md b/CITATIONS.md index e9b5164..47d7b02 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -60,6 +60,10 @@ > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0 +- [KrakenUniq](https://doi.org/10.1186/s13059-018-1568-0) + + > Breitwieser, F. P., Baker, D. N., & Salzberg, S. L. (2018). KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology, 19(1), 198. https://doi.org/10.1186/s13059-018-1568-0 + - [MALT](https://doi.org/10.1038/s41559-017-0446-6) > Vågene, Å. J., Herbig, A., Campana, M. G., Robles García, N. M., Warinner, C., Sabin, S., Spyrou, M. A., Andrades Valtueña, A., Huson, D., Tuross, N., Bos, K. I., & Krause, J. (2018). Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution, 2(3), 520–528. https://doi.org/10.1038/s41559-017-0446-6 diff --git a/README.md b/README.md index d43e6a0..545b2f8 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,7 @@ - [DIAMOND](https://doi.org/10.1038/nmeth.3176) - [Kaiju](https://doi.org/10.1038/ncomms11257) - [Kraken2](https://doi.org/10.1186/s13059-019-1891-0) + - [KrakenUniq](https://doi.org/10.1186/s13059-018-1568-0) - [MALT](https://doi.org/10.1038/s41559-017-0446-6) ## Usage diff --git a/conf/test.config b/conf/test.config index 4046af5..d892f8f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,7 +16,7 @@ params { // Limit resources so that this can run on GitHub Actions max_cpus = 2 - max_memory = '6.GB' + max_memory = '14.GB' max_time = '6.h' // Input data @@ -26,12 +26,13 @@ params { dbname = "database" + build_bracken = true build_diamond = true build_kaiju = true build_malt = true build_centrifuge = true build_kraken2 = true - build_bracken = true + build_krakenuniq = true accession2taxid = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/nucl_gb.accession2taxid' nucl2taxid = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/nucl2tax.map' @@ -40,3 +41,10 @@ params { namesdmp = params.pipelines_testdata_base_path + 'createtaxdb/data/taxonomy/names.dmp' malt_mapdb = 's3://ngi-igenomes/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip' } + +process { + withName:'KRAKENUNIQ_BUILD'{ + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + ext.args = "--work-on-disk --max-db-size 14 --kmer-len 15 --minimizer-len 13 --jellyfish-bin \$(which jellyfish)" + } +} diff --git a/conf/test_full.config b/conf/test_full.config index b43690d..a628fd1 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -19,11 +19,11 @@ params { // TODO nf-core: Give any required params for the test so that command line flags are not needed input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + build_bracken = true build_diamond = true build_kaiju = true build_malt = true build_centrifuge = true build_kraken2 = true - build_bracken = true - + build_krakenuniq = true } diff --git a/conf/test_nothing.config b/conf/test_nothing.config index 4fd0e0f..b290707 100644 --- a/conf/test_nothing.config +++ b/conf/test_nothing.config @@ -25,11 +25,11 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/createtaxdb/samplesheets/test.csv' + build_bracken = false build_diamond = false build_kaiju = false build_malt = false build_centrifuge = false build_kraken2 = false - build_bracken = false - + build_krakenuniq = false } diff --git a/docs/output.md b/docs/output.md index 1a30100..9f5ddb0 100644 --- a/docs/output.md +++ b/docs/output.md @@ -19,6 +19,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [DIAMOND](#diamond) - Database files for DIAMOND - [Kaiju](#kaiju) - Database files for Kaiju - [Kraken2](#kraken2) - Database files for Kraken2 +- [KrakenUniq](#krakenuniq) - Database files for KrakenUniq - [MALT](#malt) - Database files for MALT ### MultiQC @@ -139,6 +140,24 @@ The `fmi` file can be given to Kaiju itself with `kaiju -f .fmi` The resulting `/` directory can be given to Kraken2 itself with `kraken2 --db ` etc. +### KrakenUniq + +[KrakenUniq](https://github.com/fbreitwieser/krakenuniq) Metagenomics classifier with unique k-mer counting for more specific results. + +
+Output files + +- `kraken2/` + - `/` + - `database-build.log`: KrakenUniq build process log + - `database.idx`: KrakenUniq index file + - `database.kdb`: KrakenUniq database file + - `taxDB`: KrakenUniq taxonomy information file + +
+ +Note there may be additional files in this directory, however the ones listed above are the reportedly the required ones. + ### MALT [MALT](https://software-ab.cs.uni-tuebingen.de/download/malt) is a fast replacement for BLASTX, BLASTP and BLASTN, and provides both local and semi-global alignment capabilities. diff --git a/modules.json b/modules.json index a318afd..188eb8b 100644 --- a/modules.json +++ b/modules.json @@ -50,6 +50,12 @@ "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2", "installed_by": ["fasta_build_add_kraken2_bracken"] }, + "krakenuniq/build": { + "branch": "master", + "git_sha": "e3857325a14ef6e50e33c104c0a3be0ccaabbeb1", + "installed_by": ["modules"], + "patch": "modules/nf-core/krakenuniq/build/krakenuniq-build.diff" + }, "malt/build": { "branch": "master", "git_sha": "7d3bac628092d1aead36960c4b6ae41302a9f797", diff --git a/modules/nf-core/krakenuniq/build/environment.yml b/modules/nf-core/krakenuniq/build/environment.yml new file mode 100644 index 0000000..d99b5ef --- /dev/null +++ b/modules/nf-core/krakenuniq/build/environment.yml @@ -0,0 +1,7 @@ +name: krakenuniq_build +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::krakenuniq=1.0.4 diff --git a/modules/nf-core/krakenuniq/build/krakenuniq-build.diff b/modules/nf-core/krakenuniq/build/krakenuniq-build.diff new file mode 100644 index 0000000..9fd794c --- /dev/null +++ b/modules/nf-core/krakenuniq/build/krakenuniq-build.diff @@ -0,0 +1,14 @@ +Changes in module 'nf-core/krakenuniq/build' +--- modules/nf-core/krakenuniq/build/main.nf ++++ modules/nf-core/krakenuniq/build/main.nf +@@ -8,7 +8,7 @@ + 'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2' }" + + input: +- tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy"), path(custom_seqid2taxid) ++ tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy/*"), path(custom_seqid2taxid) + + output: + tuple val(meta), path("$prefix/"), emit: db + +************************************************************ diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf new file mode 100644 index 0000000..c55dd4d --- /dev/null +++ b/modules/nf-core/krakenuniq/build/main.nf @@ -0,0 +1,37 @@ +process KRAKENUNIQ_BUILD { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.4--pl5321h6dccd9a_2': + 'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2' }" + + input: + tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy/*"), path(custom_seqid2taxid) + + output: + tuple val(meta), path("$prefix/"), emit: db + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + custom_db = custom_library_dir ? "mkdir $prefix && mv library taxonomy $custom_seqid2taxid $prefix" : "" + """ + $custom_db + + krakenuniq-build \\ + $args \\ + --threads ${task.cpus} \\ + --db ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/krakenuniq/build/meta.yml b/modules/nf-core/krakenuniq/build/meta.yml new file mode 100644 index 0000000..f63b325 --- /dev/null +++ b/modules/nf-core/krakenuniq/build/meta.yml @@ -0,0 +1,48 @@ +name: "krakenuniq_build" +description: Download and build (custom) KrakenUniq databases +keywords: + - metagenomics + - krakenuniq + - database + - build + - ncbi +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 + tool_dev_url: 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 ] + - custom_library_dir: + type: directory + description: Optional directory containing custom fasta files for database build + pattern: "*" + - custom_taxonomy_dir: + type: directory + description: Optional directory containing custom taxonomy files for database build + 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" + - db: + type: directory + description: Directory containing KrakenUniq database + pattern: "*/" +authors: + - "@jfy133" +maintainers: + - "@jfy133" diff --git a/nextflow.config b/nextflow.config index 15cec1c..e26941f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -65,6 +65,7 @@ params { malt_mapdb = null // tool specific options + build_bracken = false build_diamond = false build_kaiju = false build_malt = false @@ -72,7 +73,7 @@ params { build_centrifuge = false build_kraken2 = false kraken2_keepintermediate = false - build_bracken = false + build_krakenuniq = false } // Load base.config by default for all pipelines diff --git a/nextflow_schema.json b/nextflow_schema.json index 853449f..421a174 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -107,6 +107,12 @@ "description": "", "default": "", "properties": { + "build_bracken": { + "type": "boolean", + "fa_icon": "fas fa-save", + "description": "Turn on extending of Kraken2 database to include Bracken files. Requires nucleotide FASTA File input.", + "help_text": "Bracken2 databases are simply just a Kraken2 database with two additional files.\n\nNote however this requires a Kraken2 database _with_ intermediate files still in it, thus can result in large database directories." + }, "build_centrifuge": { "type": "boolean", "description": "Turn on building of Centrifuge database. Requires nucleotide FASTA file input.", @@ -145,11 +151,10 @@ "fa_icon": "fas fa-save", "description": "Retain intermediate Kraken2 build files for inspection." }, - "build_bracken": { + "build_krakenuniq": { "type": "boolean", - "fa_icon": "fas fa-save", - "description": "Turn on extending of Kraken2 database to include Bracken files. Requires nucleotide FASTA File input.", - "help_text": "Bracken2 databases are simply just a Kraken2 database with two additional files.\n\nNote however this requires a Kraken2 database _with_ intermediate files still in it, thus can result in large database directories." + "fa_icon": "fas fa-toggle-on", + "description": "Turn on building of KrakenUniq database. Requires nucleotide FASTA file input." } }, "fa_icon": "fas fa-database" diff --git a/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf b/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf index adf9a3d..e6431de 100644 --- a/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf @@ -199,6 +199,7 @@ def toolCitationText() { params.build_diamond ? "DIAMOND (Buchfink et al. 2015)," : "", params.build_kaiju ? "Kaiju (Menzel et al. 2016)," : "", params.build_kraken2 ? "Kraken2 (Wood et al. 2019)," : "", + params.build_krakenuniq ? "KrakenUniq (Breitwieser et al. 2018)," : "", params.build_malt ? "MALT (Vågene et al. 2018)," : "", "and MultiQC (Ewels et al. 2016)", "." @@ -217,7 +218,9 @@ def toolBibliographyText() { params.build_diamond ? "
  • Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59–60. 10.1038/nmeth.3176
    • " : "", params.build_kaiju ? "
  • Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 7, 11257. 10.1038/ncomms11257
    • " : "", params.build_kraken2 ? "
  • Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. 10.1186/s13059-019-1891-0
    • " : "", - params.build_malt ? "
  • Vågene, Å. J., Herbig, A., Campana, M. G., Robles García, N. M., Warinner, C., Sabin, S., Spyrou, M. A., Andrades Valtueña, A., Huson, D., Tuross, N., Bos, K. I., & Krause, J. (2018). Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution, 2(3), 520–528. 10.1038/s41559-017-0446-6
    • " : "", "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + params.build_krakenuniq ? "
  • Breitwieser, F. P., Baker, D. N., & Salzberg, S. L. (2018). KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology, 19(1), 198. 10.1186/s13059-018-1568-0
    • " : "", + params.build_malt ? "
  • Vågene, Å. J., Herbig, A., Campana, M. G., Robles García, N. M., Warinner, C., Sabin, S., Spyrou, M. A., Andrades Valtueña, A., Huson, D., Tuross, N., Bos, K. I., & Krause, J. (2018). Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution, 2(3), 520–528. 10.1038/s41559-017-0446-6
    • " : "", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " ].join(' ').trim() return reference_text diff --git a/tests/test.nf.test b/tests/test.nf.test index 54bea3e..76a073c 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -18,15 +18,19 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot( + file("$outputDir/bracken/database/database100mers.kmer_distrib").name, + file("$outputDir/bracken/database/database100mers.kraken").name, + file("$outputDir/bracken/database/database.kraken").name, path("$outputDir/centrifuge/"), path("$outputDir/diamond/database.dmnd"), path("$outputDir/kaiju/database.fmi"), path("$outputDir/kraken2/database/hash.k2d"), file("$outputDir/kraken2/database/opts.k2d").name, path("$outputDir/kraken2/database/taxo.k2d"), - file("$outputDir/bracken/database/database100mers.kmer_distrib").name, - file("$outputDir/bracken/database/database100mers.kraken").name, - file("$outputDir/bracken/database/database.kraken").name, + path("$outputDir/krakenuniq/database/database-build.log").readLines().last().contains('database.idx'), + file("$outputDir/krakenuniq/database/database.idx").name, + file("$outputDir/krakenuniq/database/database.kdb"), + file("$outputDir/krakenuniq/database/taxDB"), path("$outputDir/malt/malt-build.log").readLines().last().contains('Peak memory'), path("$outputDir/malt/malt_index/index0.idx"), path("$outputDir/malt/malt_index/ref.db"), diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index bf9427f..8e3bb52 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -1,6 +1,9 @@ { "test_profile": { "content": [ + "database100mers.kmer_distrib", + "database100mers.kraken", + "database.kraken", [ "database.1.cf:md5,1481615ab90b5573f6d9e57f97890178", "database.2.cf:md5,d50fa66e215e80284314ff6521dcd4a4", @@ -12,9 +15,10 @@ "hash.k2d:md5,01122a04dcef29ceb3baa68a9f6e6ef5", "opts.k2d", "taxo.k2d:md5,cd8170a8c5a1b763a9ac1ffa2107cc88", - "database100mers.kmer_distrib", - "database100mers.kraken", - "database.kraken", + true, + "database.idx", + "database.kdb:md5,a24fce43bedbc6c420f6e36d10c112a3", + "taxDB:md5,1aed1afa948daffc236deba1c5d635db", true, "index0.idx:md5,876139dc930e68992cd2625e08bba48a", "ref.db:md5,377073f58a9f9b85acca59fcf21744a9", @@ -26,8 +30,8 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-23T08:15:27.641419595" + "timestamp": "2024-05-30T10:54:40.551963562" } } \ No newline at end of file diff --git a/workflows/createtaxdb.nf b/workflows/createtaxdb.nf index 864e47c..3b5e155 100644 --- a/workflows/createtaxdb.nf +++ b/workflows/createtaxdb.nf @@ -5,16 +5,21 @@ */ include { MULTIQC } from '../modules/nf-core/multiqc/main' + +// Preprocessing +include { GUNZIP as GUNZIP_DNA } from '../modules/nf-core/gunzip/main' +include { PIGZ_COMPRESS as PIGZ_COMPRESS_DNA } from '../modules/nf-core/pigz/compress/main' +include { PIGZ_COMPRESS as PIGZ_COMPRESS_AA } from '../modules/nf-core/pigz/compress/main' include { CAT_CAT as CAT_CAT_DNA } from '../modules/nf-core/cat/cat/main' include { CAT_CAT as CAT_CAT_AA } from '../modules/nf-core/cat/cat/main' + +// Database building (with specific auxiliary modules) include { CENTRIFUGE_BUILD } from '../modules/nf-core/centrifuge/build/main' -include { KAIJU_MKFMI } from '../modules/nf-core/kaiju/mkfmi/main' include { DIAMOND_MAKEDB } from '../modules/nf-core/diamond/makedb/main' -include { MALT_BUILD } from '../modules/nf-core/malt/build/main' -include { GUNZIP as GUNZIP_DNA } from '../modules/nf-core/gunzip/main' -include { PIGZ_COMPRESS as PIGZ_COMPRESS_DNA } from '../modules/nf-core/pigz/compress/main' -include { PIGZ_COMPRESS as PIGZ_COMPRESS_AA } from '../modules/nf-core/pigz/compress/main' +include { KAIJU_MKFMI } from '../modules/nf-core/kaiju/mkfmi/main' +include { KRAKENUNIQ_BUILD } from '../modules/nf-core/krakenuniq/build/main' include { UNZIP } from '../modules/nf-core/unzip/main' +include { MALT_BUILD } from '../modules/nf-core/malt/build/main' include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' @@ -53,7 +58,7 @@ workflow CREATETAXDB { // PREPARE: Prepare input for single file inputs modules - if ( [params.build_malt, params.build_centrifuge, params.build_kraken2, params.build_bracken].any() ) { // Pull just DNA sequences + if ( [params.build_malt, params.build_centrifuge, params.build_kraken2, params.build_bracken, params.build_krakenuniq].any() ) { // Pull just DNA sequences ch_dna_refs_for_singleref = ch_samplesheet .map{meta, fasta_dna, fasta_aa -> [[id: params.dbname], fasta_dna]} @@ -69,12 +74,12 @@ workflow CREATETAXDB { } GUNZIP_DNA ( ch_dna_for_unzipping.zipped ) - ch_prepped_dna_fastas = GUNZIP_DNA.out.gunzip.mix(ch_dna_for_unzipping.unzipped).groupTuple() - ch_versions = ch_versions.mix(GUNZIP_DNA.out.versions.first()) + ch_prepped_dna_fastas = GUNZIP_DNA.out.gunzip.mix( ch_dna_for_unzipping.unzipped).groupTuple() + ch_versions = ch_versions.mix( GUNZIP_DNA.out.versions.first() ) // Place in single file ch_singleref_for_dna = CAT_CAT_DNA ( ch_prepped_dna_fastas ) - ch_versions = ch_versions.mix(CAT_CAT_DNA.out.versions.first()) + ch_versions = ch_versions.mix( CAT_CAT_DNA.out.versions.first() ) } // TODO: Possibly need to have a modification step to get header correct to actually run with kaiju... @@ -98,7 +103,7 @@ workflow CREATETAXDB { } PIGZ_COMPRESS_AA ( ch_aa_for_zipping.unzipped ) - ch_prepped_aa_fastas = PIGZ_COMPRESS_AA.out.archive.mix(ch_aa_for_zipping.zipped).groupTuple() + ch_prepped_aa_fastas = PIGZ_COMPRESS_AA.out.archive.mix( ch_aa_for_zipping.zipped).groupTuple() //ch_versions = ch_versions.mix( PIGZ_COMPRESS_AA.versions.first() ) ch_singleref_for_aa = CAT_CAT_AA ( ch_prepped_aa_fastas ) @@ -115,7 +120,7 @@ workflow CREATETAXDB { if ( params.build_centrifuge ) { CENTRIFUGE_BUILD ( CAT_CAT_DNA.out.file_out, ch_nucl2taxid, ch_taxonomy_nodesdmp, ch_taxonomy_namesdmp, [] ) - ch_versions = ch_versions.mix(CENTRIFUGE_BUILD.out.versions.first()) + ch_versions = ch_versions.mix( CENTRIFUGE_BUILD.out.versions.first() ) ch_centrifuge_output = CENTRIFUGE_BUILD.out.cf } else { ch_centrifuge_output = Channel.empty() @@ -125,7 +130,7 @@ workflow CREATETAXDB { if ( params.build_diamond ) { DIAMOND_MAKEDB ( CAT_CAT_AA.out.file_out, ch_prot2taxid, ch_taxonomy_nodesdmp, ch_taxonomy_namesdmp ) - ch_versions = ch_versions.mix(DIAMOND_MAKEDB.out.versions.first()) + ch_versions = ch_versions.mix( DIAMOND_MAKEDB.out.versions.first() ) ch_diamond_output = DIAMOND_MAKEDB.out.db } else { ch_diamond_output = Channel.empty() @@ -135,7 +140,7 @@ workflow CREATETAXDB { if ( params.build_kaiju ) { KAIJU_MKFMI ( CAT_CAT_AA.out.file_out ) - ch_versions = ch_versions.mix(KAIJU_MKFMI.out.versions.first()) + ch_versions = ch_versions.mix( KAIJU_MKFMI.out.versions.first() ) ch_kaiju_output = KAIJU_MKFMI.out.fmi } else { ch_kaiju_output = Channel.empty() @@ -153,6 +158,19 @@ workflow CREATETAXDB { ch_kraken2_bracken_output = Channel.empty() } + // SUBWORKFLOW: Run KRAKENUNIQ/BUILD + if ( params.build_krakenuniq ) { + + ch_taxdmpfiles_for_krakenuniq = Channel.of(ch_taxonomy_namesdmp).combine(Channel.of(ch_taxonomy_nodesdmp)).map{[it]} + ch_input_for_krakenuniq = ch_prepped_dna_fastas.combine(ch_taxdmpfiles_for_krakenuniq).map{ meta, reads, taxdump -> [ meta, reads, taxdump, ch_nucl2taxid ] }.dump(tag: 'input_to_ku') + + KRAKENUNIQ_BUILD ( ch_input_for_krakenuniq ) + ch_versions = ch_versions.mix( KRAKENUNIQ_BUILD.out.versions.first() ) + ch_krakenuniq_output = KRAKENUNIQ_BUILD.out.db + } else { + ch_krakenuniq_output = Channel.empty() + } + // Module: Run MALT/BUILD if ( params.build_malt ) { @@ -171,7 +189,7 @@ workflow CREATETAXDB { } MALT_BUILD (ch_input_for_malt, [], ch_malt_mapdb) - ch_versions = ch_versions.mix(MALT_BUILD.out.versions.first()) + ch_versions = ch_versions.mix( MALT_BUILD.out.versions.first() ) ch_malt_output = MALT_BUILD.out.index } else { ch_malt_output = Channel.empty() @@ -235,6 +253,7 @@ workflow CREATETAXDB { diamond_database = ch_diamond_output kaiju_database = ch_kaiju_output kraken2_bracken_database = ch_kraken2_bracken_output + krakenuniq_database = ch_krakenuniq_output malt_database = ch_malt_output }