# nf-core/taxprofiler ## Taxonomical profiling using `nf-core/taxprofiler` pipeline nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases. You can find a more exhaustive description and running instructions in here: [nf-co.re/taxprofiler](https://nf-co.re/taxprofiler). Here we provide with a small manual to how to prepare, for running the pipeline and running it in the Microsoft Azure environment. ## Create `samplesheet.csv` as: ``` sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta 2612,run1,ILLUMINA,2612_run1_R1.fq.gz,, 2612,run2,ILLUMINA,2612_run2_R1.fq.gz,, 2612,run3,ILLUMINA,2612_run3_R1.fq.gz,2612_run3_R2.fq.gz, ... ``` ## Create a `databases.csv` sheet as: ``` tool,db_name,db_params,db_path metaphlan,db1,,az://orange/databases/metaphlan_db motu,db2,,az://orange/databases/db_mOTU ... ``` The databases will be store in the corresponding data lake folder called databases. Until then you have to download and prepare the databases yourself. Files for Metaphlan were download from: [cmprod1.cibio.unitn.it/databases/MetaPhlAn/metaphlan_databases](http://cmprod1.cibio.unitn.it/databases/MetaPhlAn/metaphlan_databases/) For mOTUs: Needed to prepare the mOTUs database as follows: ```bash conda create --name motus conda activate motus conda install -c bioconda motus motus downloadDB ``` It got copied the database locally in here: `/Users/apca/anaconda3/envs/motus/lib/python3.9/site-packages/motus/db_mOTU` and I passed this dir to `databases.csv`. ## Example of Command line to run the pipeline outside Seqera Using Docker as contanerizing system Using only Metaphlan as reference database ```bash nextflow run nf-core/taxprofiler \ -profile az_test,docker \ --input samplesheet.csv \ --databases databases.csv \ --outdir results_100bp \ --perform_shortread_qc \ --shortread_qc_tool adapterremoval \ --save_analysis_ready_fastqs \ --shortread_qc_minlength 100 \ --perform_shortread_complexityfilter \ --perform_shortread_hostremoval \ --hostremoval_reference az://masldmice/host_genome/GCF_000001635.27_GRCm39_genomic.fna \ --perform_runmerging \ --run_metaphlan \ --run_profile_standardisation \ -w az://masldmice/work \ -with-tower \ -resume ``` ## Worth noticing - You need to add `--shortread_qc_minlength 100` to require a minimum length for read after quality control - You need to add `--save_analysis_ready_fastqs` to save the qc filetered reads before they go into classification or profiling - You need to add `--perform_runmerging` to merge different lanes of the same sample - You need to add `--run_profile_standardisation` so that all metaphlan profile of each sample get combined in a single report (This may be changed soon, follow issue: [taxprofiler#494](https://github.com/nf-core/taxprofiler/issues/494)) ## Seqera platform Notice that one parameter tells the pipeline to be monitored by Seqera platform (`-with-tower`). To do that login to Seqera platform and create a token (User tokens) clicking on the User settings button in the upper-right corner. Once created, copy it and export it in your terminal: ```bash export TOWER_ACCESS_TOKEN= ``` ## Needed to change vmType that in the nextflow.config: To meet the requirement of 12 CPUs and 72 GB of memory, we used `Standard_E16s_v3` with 16 cpus and 128GB memory ``` pools { auto { autoScale = true vmType = 'Standard_E16s_v3' } } ``` Also had to add the following code to skip a step that does not work well with Metaphlan: ``` process { withName: 'TAXPASTA_MERGE' { when = false } } ``` ## Parameters These are the parameters of the last succesful run
All parameters of nf-core/taxprofiler 1.2.3 (JSON) ```json { "shortread_complexityfilter_prinseqplusplus_mode": "entropy", "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master", "save_analysis_ready_fastqs": true, "malt_generate_megansummary": false, "plaintext_email": false, "malt_mode": "BlastN", "diamond_save_reads": false, "shortread_complexityfilter_prinseqplusplus_dustscore": 0.5, "kaiju_taxon_rank": "species", "standardisation_taxpasta_format": "tsv", "databases": "az://seqera/raw/projectname/data/databases.csv", "run_kmcp": false, "krakenuniq_ram_chunk_size": "16G", "version": false, "ganon_report_mincount": 0, "run_kraken2": false, "publish_dir_mode": "copy", "input": "az://seqera/raw/projectname/data/Metagenomics2/samplesheet_metagenomics2.csv", "perform_shortread_hostremoval": false, "krakenuniq_batch_size": 20, "shortread_qc_tool": "adapterremoval", "run_metaphlan": true, "preprocessing_qc_tool": "fastqc", "motus_save_mgc_read_counts": false, "shortread_qc_mergepairs": false, "kraken2_save_readclassifications": false, "taxpasta_add_name": false, "ganon_report_maxcount": 0, "standardisation_motus_generatebiom": false, "shortread_complexityfilter_fastp_threshold": 30, "shortread_complexityfilter_tool": "bbduk", "save_preprocessed_reads": false, "diamond_output_format": "tsv", "custom_config_version": "master", "ganon_report_type": "reads", "shortread_qc_minlength": 100, "run_centrifuge": false, "shortread_qc_skipadaptertrim": false, "longread_qc_qualityfilter_minlength": 1000, "run_profile_standardisation": false, "perform_shortread_qc": true, "ganon_report_rank": "default", "taxpasta_add_lineage": false, "perform_shortread_redundancyestimation": false, "run_krona": false, "motus_remove_ncbi_ids": false, "malt_save_reads": false, "save_runmerged_reads": false, "outdir": "az://seqera/results/smoke_scrub_malthe/metagenomics2/", "pipelines_testdata_base_path": "https://raw.githubusercontent.com/nf-core/test-datasets/", "help": false, "shortread_complexityfilter_bbduk_mask": false, "centrifuge_save_reads": false, "save_hostremoval_bam": false, "perform_runmerging": false, "run_bracken": false, "kmcp_save_search": false, "shortread_complexityfilter_bbduk_windowsize": 50, "help_full": false, "monochrome_logs": false, "ganon_report_toppercentile": 0, "ganon_save_readclassifications": false, "max_multiqc_email_size": "25.MB", "shortread_qc_dedup": false, "save_complexityfiltered_reads": false, "longread_filter_tool": "nanoq", "validate_params": true, "kaiju_expand_viruses": false, "run_diamond": false, "skip_preprocessing_qc": false, "krakenuniq_save_reads": false, "perform_longread_qc": false, "shortread_qc_includeunmerged": false, "trace_report_suffix": "2025-08-29_11-33-52", "shortread_redundancyestimation_mode": "kmer", "run_ganon": false, "longread_adapterremoval_tool": "porechop_abi", "taxpasta_ignore_errors": false, "longread_qc_skipadaptertrim": false, "shortread_complexityfilter_entropy": 0.3, "multiqc_title": "multiQC_metagenomics2", "kraken2_save_minimizers": false, "longread_qc_qualityfilter_minquality": 7, "krakenuniq_save_readclassifications": false, "longread_qc_skipqualityfilter": false, "run_kaiju": false, "kraken2_save_reads": false, "motus_use_relative_abundance": false, "run_motus": false, "save_hostremoval_index": false, "run_krakenuniq": false, "show_hidden": false, "longread_qc_qualityfilter_targetbases": 500000000, "bracken_save_intermediatekraken2": false, "taxpasta_add_rank": false, "perform_shortread_complexityfilter": true, "taxpasta_add_ranklineage": false, "perform_longread_hostremoval": false, "save_untarred_databases": false, "longread_qc_qualityfilter_keeppercent": 90, "taxpasta_add_idlineage": false, "run_malt": false, "save_hostremoval_unmapped": false } ```
## Resolved configuration on Seqera Seqera give a resolved configuration of the parameters and all settings with respect to the profile setting up the compute environment.
Resolved parameters and profile configuration of a taxprofiler 1.2.3 on Azure ``` nextflow { enable { strict = true configProcessNamesValidation = false } } params { input = 'az://seqera/raw/smoke_scrub_malthe/data/Metagenomics2/samplesheet_metagenomics2.csv' multiqc_config = null multiqc_title = 'multiQC_metagenomics2' multiqc_logo = null max_multiqc_email_size = '25.MB' multiqc_methods_description = null outdir = 'az://seqera/results/smoke_scrub_malthe/metagenomics2/' publish_dir_mode = 'copy' email = null email_on_fail = null plaintext_email = false monochrome_logs = false hook_url = null help = false help_full = false show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' trace_report_suffix = '2025-08-29_11-33-55' config_profile_name = null config_profile_description = null custom_config_version = 'master' shortread_qc_minlength = 100 perform_shortread_complexityfilter = true save_analysis_ready_fastqs = true perform_shortread_qc = true run_profile_standardisation = false run_metaphlan = true shortread_qc_tool = 'adapterremoval' databases = 'az://seqera/raw/smoke_scrub_malthe/data/databases.csv' custom_config_base = 'https://raw.githubusercontent.com/nf-core/configs/master' config_profile_contact = null config_profile_url = null validate_params = true save_untarred_databases = false skip_preprocessing_qc = false preprocessing_qc_tool = 'fastqc' shortread_qc_skipadaptertrim = false shortread_qc_mergepairs = false shortread_qc_includeunmerged = false shortread_qc_adapter1 = null shortread_qc_adapter2 = null shortread_qc_adapterlist = null shortread_qc_dedup = false perform_longread_qc = false longread_adapterremoval_tool = 'porechop_abi' longread_qc_skipadaptertrim = false longread_qc_skipqualityfilter = false longread_filter_tool = 'nanoq' longread_qc_qualityfilter_minlength = 1000 longread_qc_qualityfilter_keeppercent = 90 longread_qc_qualityfilter_minquality = 7 longread_qc_qualityfilter_targetbases = 500000000 save_preprocessed_reads = false perform_shortread_redundancyestimation = false shortread_redundancyestimation_mode = 'kmer' shortread_complexityfilter_tool = 'bbduk' shortread_complexityfilter_entropy = 0.3 shortread_complexityfilter_bbduk_windowsize = 50 shortread_complexityfilter_bbduk_mask = false shortread_complexityfilter_prinseqplusplus_mode = 'entropy' shortread_complexityfilter_prinseqplusplus_dustscore = 0.5 shortread_complexityfilter_fastp_threshold = 30 save_complexityfiltered_reads = false perform_runmerging = false save_runmerged_reads = false perform_shortread_hostremoval = false perform_longread_hostremoval = false hostremoval_reference = null shortread_hostremoval_index = null longread_hostremoval_index = null save_hostremoval_index = false save_hostremoval_bam = false save_hostremoval_unmapped = false run_malt = false malt_mode = 'BlastN' malt_generate_megansummary = false malt_save_reads = false run_kraken2 = false kraken2_save_reads = false kraken2_save_readclassifications = false kraken2_save_minimizers = false run_krakenuniq = false krakenuniq_ram_chunk_size = '16G' krakenuniq_save_reads = false krakenuniq_save_readclassifications = false krakenuniq_batch_size = 20 run_bracken = false bracken_save_intermediatekraken2 = false run_centrifuge = false centrifuge_save_reads = false run_kaiju = false kaiju_expand_viruses = false kaiju_taxon_rank = 'species' run_diamond = false diamond_output_format = 'tsv' diamond_save_reads = false run_motus = false motus_use_relative_abundance = false motus_remove_ncbi_ids = false motus_save_mgc_read_counts = false run_kmcp = false kmcp_save_search = false run_ganon = false ganon_report_type = 'reads' ganon_report_rank = 'default' ganon_report_toppercentile = 0 ganon_report_mincount = 0 ganon_report_maxcount = 0 ganon_save_readclassifications = false run_krona = false krona_taxonomy_directory = null standardisation_taxpasta_format = 'tsv' taxpasta_taxonomy_dir = null taxpasta_add_name = false taxpasta_add_rank = false taxpasta_add_lineage = false taxpasta_add_idlineage = false taxpasta_add_ranklineage = false taxpasta_ignore_errors = false standardisation_motus_generatebiom = false } process { cpus = { 1 * task.attempt } memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' withLabel:process_single { cpus = { 1 } memory = { 1.GB * task.attempt } time = { 4.h * task.attempt } } withLabel:process_low { cpus = { 2 * task.attempt } memory = { 12.GB * task.attempt } time = { 4.h * task.attempt } } withLabel:process_medium { cpus = { 6 * task.attempt } memory = { 36.GB * task.attempt } time = { 8.h * task.attempt } } withLabel:process_high { cpus = { 12 * task.attempt } memory = { 72.GB * task.attempt } time = { 16.h * task.attempt } } withLabel:process_long { time = { 20.h * task.attempt } } withLabel:process_high_memory { memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' } withLabel:error_retry { errorStrategy = 'retry' maxRetries = 2 } withName:BRACKEN_BRACKEN { errorStrategy = 'ignore' tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure34$_closure70@407d2a01 } publishDir = [path:{ "${params.outdir}/bracken/${meta.db_name}/" }, mode:'copy', pattern:'*{.tsv,.txt}'] } withName:CENTRIFUGE_KREPORT { errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'} tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure46$_closure78@461b38ca } publishDir = [path:{ "${params.outdir}/centrifuge/${meta.db_name}/" }, mode:'copy', pattern:'*.{txt}'] } withName:KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE { errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' } ext { prefix = { "centrifuge_${meta.id}_combined_reports" } } publishDir = [path:{ "${params.outdir}/centrifuge/" }, mode:'copy', pattern:'*.{txt}'] } withName:MEGAN_RMA2INFO_TSV { cpus = { 1 } memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } tag = {"${meta.db_name}|${meta.id}"} ext { args = '-c2c Taxonomy' prefix = { "${meta.id}" } } publishDir = [path:{ "${params.outdir}/malt/${meta.db_name}/" }, mode:'copy', pattern:'*.{txt.gz,megan}'] } withName:MEGAN_RMA2INFO_KRONA { cpus = { 1 } memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } tag = {"${meta.db_name}|${meta.id}"} ext { args = { "--read2class Taxonomy" } prefix = { "${meta.id}_${meta.db_name}" } } } withName:FALCO { cpus = { 6 } memory = { 4.GB * task.attempt } time = { 4.h * task.attempt } ext { prefix = { "${meta.id}_${meta.run_accession}_raw_falco" } } publishDir = [path:{ "${params.outdir}/falco/raw" }, mode:'copy', pattern:'*.{html,txt,zip}'] } publishDir = [path:{ "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }] withName:UNTAR { ext { prefix = { "${archive.simpleName}" } } publishDir = [path:{ "${params.outdir}/untar/databases" }, mode:'copy', enabled:false] } withName:FASTQC { ext { args = '--quiet' prefix = { "${meta.id}_${meta.run_accession}_raw" } } publishDir = [path:{ "${params.outdir}/fastqc/raw" }, mode:'copy', pattern:'*.{html,zip}'] } withName:FASTQC_PROCESSED { ext { args = '--quiet' prefix = { "${meta.id}_${meta.run_accession}_processed" } } publishDir = [path:{ "${params.outdir}/fastqc/processed" }, mode:'copy', pattern:'*.{html,zip}'] } withName:FALCO_PROCESSED { ext { prefix = { "${meta.id}_${meta.run_accession}_processed_falco" } } publishDir = [path:{ "${params.outdir}/falco/processed" }, mode:'copy', pattern:'*.{html,txt,zip}'] } withName:FASTP_SINGLE { ext { args = '--length_required 100' prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/fastp" }, mode:'copy', pattern:'*.fastq.gz', enabled:false], [path:{ "${params.outdir}/fastp" }, mode:'copy', pattern:'*.{log,html,json}'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:FASTP_PAIRED { ext { args = '--detect_adapter_for_pe --length_required 100' prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/fastp" }, mode:'copy', pattern:'*.fastq.gz', enabled:false], [path:{ "${params.outdir}/fastp" }, mode:'copy', pattern:'*.{log,html,json}'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*.fastp.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:ADAPTERREMOVAL_SINGLE { ext { args = '--minlength 100' prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/adapterremoval" }, mode:'copy', pattern:'*.fastq.gz', enabled:false], [path:{ "${params.outdir}/adapterremoval" }, mode:'copy', pattern:'*.settings'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*truncated.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:ADAPTERREMOVAL_PAIRED { ext { args = '--minlength 100' prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/adapterremoval" }, mode:'copy', pattern:'*.fastq.gz', enabled:false], [path:{ "${params.outdir}/adapterremoval" }, mode:'copy', pattern:'*.settings'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*{truncated.fastq,singleton.truncated}.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs ? it : null}]] } withName:NONPAREIL_NONPAREIL { ext { prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [path:{ "${params.outdir}/nonpareil/" }, mode:'copy', pattern:'*.np{a,c,l,o}'] } withName:NONPAREIL_CURVE { ext { prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [path:{ "${params.outdir}/nonpareil/" }, mode:'copy', pattern:'*.png'] } withName:NONPAREIL_SET { ext { prefix = { "nonpareil_all_samples_mqc" } } publishDir = [path:{ "${params.outdir}/nonpareil/" }, mode:'copy', pattern:'*.png'] } withName:NONPAREIL_NONPAREILCURVESR { ext { prefix = { "nonpareil_all_samples" } } publishDir = [path:{ "${params.outdir}/nonpareil/" }, mode:'copy', pattern:'*.{json,csv,tsv,pdf}'] } withName:CAT_FASTQ { ext { prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:PORECHOP_PORECHOP { ext { prefix = { "${meta.id}_${meta.run_accession}_porechop" } } publishDir = [[path:{ "${params.outdir}/porechop" }, mode:'copy', pattern:'*_porechop.fastq.gz', enabled:false], [path:{ "${params.outdir}/porechop" }, mode:'copy', pattern:'*.log'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*_porechop.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:PORECHOP_ABI { ext { prefix = { "${meta.id}_${meta.run_accession}_porechop_abi" } } publishDir = [[path:{ "${params.outdir}/porechop_abi" }, mode:'copy', pattern:'*_porechop_abi.fastq.gz', enabled:false], [path:{ "${params.outdir}/porechop_abi" }, mode:'copy', pattern:'*.log'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*porechop_abi.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:FILTLONG { ext { args = '--min_length 1000 --keep_percent 90 --target_bases 500000000' prefix = { "${meta.id}_${meta.run_accession}_filtered" } } publishDir = [[path:{ "${params.outdir}/filtlong" }, mode:'copy', pattern:'*.fastq.gz', enabled:false], [path:{ "${params.outdir}/filtlong" }, mode:'copy', pattern:'*.log'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:NANOQ { ext { args = '-vv --min-len 1000 --min-qual 7' prefix = { "${meta.id}_${meta.run_accession}_filtered" } } publishDir = [[path:{ "${params.outdir}/nanoq" }, mode:'copy', pattern:'*_filtered.fastq.gz', enabled:false], [path:{ "${params.outdir}/nanoq" }, mode:'copy', pattern:'*_filtered.stats'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*_filtered.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null }]] } withName:BBMAP_BBDUK { ext { args = 'entropy=0.3 entropywindow=50 entropymask=f' prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/bbduk/" }, mode:'copy', pattern:'*.{fastq.gz}', enabled:false], [path:{ "${params.outdir}/bbduk/" }, mode:'copy', pattern:'*.log'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*.fastq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }]] } withName:PRINSEQPLUSPLUS { ext { args = '-lc_entropy=0.3 -trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0' prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/prinseqplusplus/" }, mode:'copy', pattern:'*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}', enabled:false], [path:{ "${params.outdir}/prinseqplusplus/" }, mode:'copy', pattern:'*.log'], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null }]] } withName:BOWTIE2_BUILD { publishDir = [[path:{ "${params.outdir}/bowtie2/build" }, mode:'copy', pattern:'bowtie2', enabled:false]] } withName:BOWTIE2_ALIGN { ext { prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [[path:{ "${params.outdir}/bowtie2/align" }, mode:'copy', pattern:'*.log'], [path:{ "${params.outdir}/bowtie2/align" }, mode:'copy', pattern:'*.bam', enabled:false], [path:{ "${params.outdir}/bowtie2/align" }, mode:'copy', pattern:'*.fastq.gz', enabled:false], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', enabled:true, pattern:'*.fastq.gz', saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && params.perform_shortread_hostremoval && params.save_analysis_ready_fastqs ? it : null }]] } withName:MINIMAP2_INDEX { ext { args = '-x map-ont' } publishDir = [path:{ "${params.outdir}/minimap2/index" }, mode:'copy', pattern:'*.mmi', enabled:false] } withName:MINIMAP2_ALIGN { ext { prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [path:{ "${params.outdir}/minimap2/align" }, mode:'copy', pattern:'*.bam', enabled:false] } withName:SAMTOOLS_VIEW { ext { args = '-f 4' prefix = { "${meta.id}_${meta.run_accession}.unmapped" } } } withName:SAMTOOLS_FASTQ { ext { prefix = { "${meta.id}_${meta.run_accession}.unmapped" } } publishDir = [[path:{ "${params.outdir}/samtools/fastq" }, mode:'copy', pattern:'*_other.fastq.gz', enabled:false], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*.fq.gz', enabled:true, saveAs:{ ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun) ) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null }]] } withName:SAMTOOLS_STATS { ext { prefix = { "${meta.id}_${meta.run_accession}" } } publishDir = [path:{ "${params.outdir}/samtools/stats" }, mode:'copy', pattern:'*stats'] } withName:MERGE_RUNS { ext { prefix = { "${meta.id}" } } publishDir = [[path:{ "${params.outdir}/run_merging/" }, mode:'copy', pattern:'*.fastq.gz', enabled:false], [path:{ "${params.outdir}/analysis_ready_fastqs" }, mode:'copy', pattern:'*.fastq.gz', enabled:false]] } withName:MALT_RUN { tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params} -m ${params.malt_mode}" } prefix = { "${meta.db_name}" } } publishDir = [path:{ "${params.outdir}/malt/${meta.db_name}/" }, mode:'copy', pattern:'*.{rma6,log,sam}'] } withName:KRAKEN2_KRAKEN2 { tag = { "${meta.db_name}|${meta.tool}|${meta.id}" } ext { args = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure32$_closure64@3881b884 prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure32$_closure66@1185b0b7 } publishDir = [path:{ "${params.outdir}/kraken2/${meta.db_name}/" }, mode:'copy', pattern:'*.{txt,fastq.gz}', saveAs:{ !params.bracken_save_intermediatekraken2 && meta.tool == "bracken" ? null : it }] } withName:KRAKEN2_STANDARD_REPORT { tag = { "${meta.db_name}|${meta.tool}|${meta.id}" } ext { prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure33$_closure68@ec70725 } publishDir = [path:{ "${params.outdir}/kraken2/${meta.db_name}/" }, mode:'copy', pattern:'*.report.txt'] } withName:BRACKEN_COMBINEBRACKENOUTPUTS { ext { prefix = { "bracken_${meta.id}_combined_reports" } } publishDir = [path:{ "${params.outdir}/bracken/" }, mode:'copy', pattern:'*.txt'] } withName:KRAKENTOOLS_COMBINEKREPORTS_KRAKEN { ext { prefix = { "kraken2_${meta.id}_combined_reports" } } publishDir = [path:{ "${params.outdir}/kraken2/" }, mode:'copy', pattern:'*.txt'] } withName:KRAKENUNIQ_PRELOADEDKRAKENUNIQ { tag = { "${meta.db_name}|${task.index}" } ext { args = { "${meta.db_params}" } prefix = { "${meta.db_name}.krakenuniq" } } publishDir = [path:{ "${params.outdir}/krakenuniq/${meta.db_name}/" }, mode:'copy', pattern:'*.{txt,fastq.gz,fasta.gz}'] } withName:KRAKENTOOLS_KREPORT2KRONA { publishDir = [enabled:false, mode:'copy', pattern:'*.txt'] } withName:KRONA_CLEANUP { ext { prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure39$_closure72@2082e0e4 } publishDir = [path:{ "${params.outdir}/krona/" }, mode:'copy', pattern:'*.{html}'] } withName:KRONA_KTIMPORTTEXT { ext { prefix = { "${meta.tool}_${meta.id}" } } publishDir = [path:{ "${params.outdir}/krona/" }, mode:'copy', pattern:'*.{html}'] } withName:KRONA_KTIMPORTTAXONOMY { ext { args = '-i' prefix = { "${meta.tool}_${meta.id}" } } publishDir = [path:{ "${params.outdir}/krona/" }, mode:'copy', pattern:'*.{html}'] } withName:METAPHLAN_METAPHLAN { tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure43$_closure74@15f229e8 } publishDir = [path:{ "${params.outdir}/metaphlan/${meta.db_name}/" }, mode:'copy', pattern:'*.{biom,txt}'] } withName:METAPHLAN_MERGEMETAPHLANTABLES { ext { prefix = { "metaphlan_${meta.id}_combined_reports" } } publishDir = [path:{ "${params.outdir}/metaphlan/" }, mode:'copy', pattern:'*.{txt}'] } withName:CENTRIFUGE_CENTRIFUGE { tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure45$_closure76@29ce33e9 } publishDir = [path:{ "${params.outdir}/centrifuge/${meta.db_name}/" }, mode:'copy', pattern:'*.{txt,sam,tab,gz}'] } withName:KAIJU_KAIJU { tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure48$_closure80@1f86f7da } publishDir = [path:{ "${params.outdir}/kaiju/${meta.db_name}/" }, mode:'copy', pattern:'*.tsv'] } withName:KAIJU_KAIJU2TABLE_SINGLE { tag = {"${meta.db_name}|${meta.id}"} ext { args = {[ params.kaiju_expand_viruses ? "-e" : "" ].join(' ').trim() } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure49$_closure82@28b4b10e } publishDir = [path:{ "${params.outdir}/kaiju/${meta.db_name}/" }, mode:'copy', pattern:'*.{txt}'] } withName:KAIJU_KAIJU2TABLE_COMBINED { ext { prefix = { "kaiju_${meta.id}_combined_reports" } } publishDir = [path:{ "${params.outdir}/kaiju/" }, mode:'copy', pattern:'*.{txt}'] } withName:KAIJU_KAIJU2KRONA { tag = {"${meta.db_name}|${meta.id}"} ext { args = '-v -u' } publishDir = [path:{ "${params.outdir}/kaiju/" }, enabled:false] } withName:DIAMOND_BLASTX { tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure52$_closure84@2c0d7099 } publishDir = [path:{ "${params.outdir}/diamond/${meta.db_name}/" }, mode:'copy', pattern:'*.{blast,xml,txt,daa,sam,tsv,paf,log}'] } withName:MOTUS_PROFILE { tag = {"${meta.db_name}|${meta.id}"} ext { args = { [ params.motus_remove_ncbi_ids ? "" : "-p", params.motus_use_relative_abundance ? "" : "-c", params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : "" ].join(',').replaceAll(','," ") } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure53$_closure86@74844f8a } publishDir = [path:{ "${params.outdir}/motus/${meta.db_name}/" }, mode:'copy'] } withName:MOTUS_MERGE { ext { args = { params.standardisation_motus_generatebiom ? "-B" : "" } prefix = { "motus_${meta.id}_combined_reports" } } publishDir = [path:{ "${params.outdir}/motus/" }, mode:'copy'] } withName:KMCP_SEARCH { tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure55$_closure88@5c945ee7 } publishDir = [path:{ "${params.outdir}/kmcp/${meta.db_name}/" }, mode:'copy', enabled:false] } withName:KMCP_PROFILE { tag = {"${meta.db_name}|${meta.id}"} ext { args = { "${meta.db_params}" } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure56$_closure90@51a5a8ba } publishDir = [path:{ "${params.outdir}/kmcp/${meta.db_name}/" }, mode:'copy', pattern:'*.{profile}'] } withName:GANON_CLASSIFY { tag = {"${meta.db_name}|${meta.id}"} ext { args = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure57$_closure92@16eb93af prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure57$_closure94@404566e7 } publishDir = [path:{ "${params.outdir}/ganon/${meta.db_name}/" }, mode:'copy', pattern:'*.{tre,rep,one,all,unc,log}'] } withName:GANON_REPORT { tag = {"${meta.db_name}|${meta.id}"} ext { args = {[ "--report-type ${params.ganon_report_type}", ganon_report_rank != 'default' ? "--ranks ${params.ganon_report_rank}" : "", "--top-percentile ${params.ganon_report_toppercentile}", "--min-count ${params.ganon_report_mincount}", "--max-count ${params.ganon_report_maxcount}" ].join(' ').trim() } prefix = Script678F515BC912152A583104ACD4973692$_run_closure1$_closure58$_closure96@3ed87b6e } publishDir = [path:{ "${params.outdir}/ganon/${meta.db_name}/" }, mode:'copy', pattern:'*.{tre}'] } withName:GANON_TABLE { ext { prefix = { "ganon_${meta.id}_combined_reports" } } publishDir = [path:{ "${params.outdir}/ganon/" }, mode:'copy', pattern:'*.txt'] } withName:TAXPASTA_MERGE { tag = { "${meta.tool}|${meta.id}" } ext { prefix = { "${meta.tool}_${meta.id}" } args = { [ params.taxpasta_add_name ? "--add-name" : "", params.taxpasta_add_rank ? "--add-rank" : "", params.taxpasta_add_lineage ? "--add-lineage" : "", params.taxpasta_add_idlineage ? "--add-id-lineage" : "", params.taxpasta_add_ranklineage ? "--add-rank-lineage" : "", ].join(' ').trim() } } publishDir = [path:{ "${params.outdir}/taxpasta/" }, mode:'copy', pattern:'*.{tsv,csv,arrow,parquet,biom}'] } withName:TAXPASTA_STANDARDISE { tag = { "${meta.tool}|${meta.id}" } ext { prefix = { "${meta.tool}_${meta.id}" } args = { [ params.taxpasta_add_name ? "--add-name" : "", params.taxpasta_add_rank ? "--add-rank" : "", params.taxpasta_add_lineage ? "--add-lineage" : "", params.taxpasta_add_idlineage ? "--add-id-lineage" : "", params.taxpasta_add_ranklineage ? "--add-rank-lineage" : "" ].join(' ').trim() } } publishDir = [path:{ "${params.outdir}/taxpasta/" }, mode:'copy', pattern:'*.{tsv,csv,arrow,parquet,biom}'] } withName:MULTIQC { ext { args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } } publishDir = [path:{ "${params.outdir}/multiqc" }, mode:'copy', saveAs:{ filename -> filename.equals('versions.yml') ? null : filename }] } shell = ['bash', '-C', '-e', '-u', '-o', 'pipefail'] executor = 'azurebatch' queue = 'pool-Standard_E16ds_v4-pack' } apptainer { registry = 'quay.io' } docker { registry = 'quay.io' } podman { registry = 'quay.io' } singularity { registry = 'quay.io' } charliecloud { registry = 'quay.io' } env { PYTHONNOUSERSITE = '1' R_PROFILE_USER = '/.Rprofile' R_ENVIRON_USER = '/.Renviron' JULIA_DEPOT_PATH = '/usr/local/share/julia' } timeline { enabled = true file = 'timeline-23Nhgz2D50ZhCR.html' } report { enabled = true file = 'az://seqera/results/smoke_scrub_malthe/metagenomics2//pipeline_info/execution_report_2025-08-29_11-33-55.html' } trace { enabled = true file = 'az://seqera/results/smoke_scrub_malthe/metagenomics2//pipeline_info/execution_trace_2025-08-29_11-33-55.txt' } dag { enabled = true file = 'az://seqera/results/smoke_scrub_malthe/metagenomics2//pipeline_info/pipeline_dag_2025-08-29_11-33-55.html' } manifest { name = 'nf-core/taxprofiler' author = 'James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li, and the nf-core/taxprofiler team' contributors = [[name:'James A. Fellows Yates', affiliation:'Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany', email:'jfy133@gmail.com', github:'https://github.com/jfy133', contribution:['author', 'maintainer'], orcid:'https://orcid.org/0000-0001-5585-6277'], [name:'Sofia Stamouli', affiliation:'Karolinska Institutet/Karolinska University Hospital/Clinical Genomics SciLifeLab, Solna, Sweden', email:'', github:'https://github.com/sofstam', contribution:['author', 'maintainer'], orcid:'https://orcid.org/0009-0006-0893-3771'], [name:'Moritz E. Beber', affiliation:'Unseen Bio ApS, Copenhagen, Denmark​', email:'', github:'https://github.com/Midnighter', contribution:['author', 'maintainer'], orcid:'https://orcid.org/0000-0003-2406-1978'], [name:'Lili Andersson-Li', affiliation:'Karolinska Institutet/Karolinska University Hospital/Clinical Genomics SciLifeLab, Solna, Sweden', email:'', github:'https://github.com/LilyAnderssonLee', contribution:['author', 'maintainer'], orcid:'https://orcid.org/0000-0002-6059-4192'], [name:'and the nf-core/taxprofiler team', affiliation:'nf-core community', email:'', github:'https://github.com/nf-core', contribution:['contributor'], orcid:'']] homePage = 'https://github.com/nf-core/taxprofiler' description = 'Taxonomic classification and profiling of shotgun short- and long-read metagenomic data' mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' version = '1.2.3' doi = '10.1101/2023.10.20.563221' } plugins = ['nf-schema@2.3.0'] validation { monochromeLogs = false help { enabled = true command = 'nextflow run nf-core/taxprofiler -profile --input samplesheet.csv --outdir ' fullParameter = 'help_full' showHiddenParameter = 'show_hidden' beforeText = ' ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/taxprofiler 1.2.3 ------------------------------------------------------ ' afterText = ' * The pipeline https://doi.org/10.1101/2023.10.20.563221 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/taxprofiler/blob/master/CITATIONS.md ' } summary { beforeText = ' ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/taxprofiler 1.2.3 ------------------------------------------------------ ' afterText = ' * The pipeline https://doi.org/10.1101/2023.10.20.563221 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/taxprofiler/blob/master/CITATIONS.md ' } } azure { storage { accountName = 'workstoragedls' } batch { location = 'northeurope' accountName = 'batchseqeraprod' copyToolInstallMode = 'task' autoPoolMode = false allowPoolCreation = false pools { 'pool-Standard_E16ds_v4-pack' { vmType = 'standard_e16ds_v4' vmCount = 0 } } } managedIdentity { clientId = '25959159-120b-4e8e-a63a-dd9be7901124' } } workDir = 'az://seqera/scratch/2Fash9z9564Wul' runName = 'awesome_goldberg_2' resume = '22e5d9d9-1203-41a0-b6ff-e986085fd3be' tower { enabled = true endpoint = 'https://api.cloud.seqera.io' } cloudcache { enabled = true path = 'az://seqera/.cache' } ```