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…peline Re-structure pipeline
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| id: "ebi-metagenomics/emg-viral-pipeline-methods-description" | ||
| description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." | ||
| section_name: "ebi-metagenomics/emg-viral-pipeline Methods Description" | ||
| section_href: "https://github.com/EBI-Metagenomics/emg-viral-pipeline" | ||
| plot_type: "html" | ||
| data: | | ||
| <h4>Methods</h4> | ||
| <p>Data was processed using ebi-metagenomics/genomes-generation v${workflow.manifest.version} (${doi_text}; <a href="https://doi.org/10.1093/nargab/lqac007">Krakau <em>et al.</em>, 2022</a>) of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p> | ||
| <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p> | ||
| <pre><code>${workflow.commandLine}</code></pre> | ||
| <p>${tool_citations}</p> | ||
| <h4>References</h4> | ||
| <ul> | ||
| <li> | ||
| Informative Regions In Viral Genomes | ||
| <i>Viruses (2021)</i> | ||
| doi: <a href="https://doi.org/10.3390/v13061164">10.3390/v13061164</a> | ||
| Moreno-Gallego, Jaime Leonardo, and Alejandro Reyes | ||
| </li> | ||
| <li> | ||
| VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models | ||
| <i>bioRxiv</i> | ||
| doi: <a href="https://doi.org/10.1101/2022.08.22.504484">10.1101/2022.08.22.504484</a> | ||
| Rangel-Pineros, Guillermo, et al. | ||
| </li> | ||
| ${tool_bibliography} | ||
| </ul> | ||
| <div class="alert alert-info"> | ||
| <h5>Notes:</h5> | ||
| <ul> | ||
| ${nodoi_text} | ||
| <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li> | ||
| <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li> | ||
| </ul> | ||
| </div> |
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| report_comment: > | ||
| This report has been generated by the <a href="https://github.com/ebi-metagenomics/emg-viral-pipeline/" target="_blank">ebi-metagenomics/emg-viral-pipeline</a> pipeline. | ||
| report_section_order: | ||
| "ebi-metagenomics/emg-viral-pipeline-methods-description": | ||
| order: -1000 | ||
| software_versions: | ||
| order: -1001 | ||
| "ebi-metagenomics/emg-viral-pipeline-summary": | ||
| order: -1002 | ||
|
|
||
| export_plots: true | ||
|
|
||
| data_format: "yaml" | ||
|
|
||
| run_modules: | ||
| - fastqc | ||
| - fastp | ||
|
|
||
| ## Module order | ||
| module_order: | ||
| - fastqc | ||
| - fastp | ||
|
|
||
| ## File name cleaning | ||
| extra_fn_clean_exts: | ||
| - "_fastp" | ||
|
|
||
| ## Prettification | ||
| custom_logo: "mgnify_logo.png" | ||
| custom_logo_url: https://github.com/ebi-metagenomics/emg-viral-pipeline/ | ||
| custom_logo_title: "ebi-metagenomics/emg-viral-pipeline" | ||
|
|
||
| ## General Stats customisation | ||
| table_columns_visible: | ||
| "fastp": | ||
| pct_duplication: False | ||
| after_filtering_q30_rate: False | ||
| after_filtering_q30_bases: False | ||
| filtering_result_passed_filter_reads: 3300 | ||
| after_filtering_gc_content: False | ||
| pct_surviving: True | ||
| pct_adapter: True | ||
|
|
||
| table_columns_placement: | ||
| "fastp": | ||
| pct_duplication: 3000 | ||
| after_filtering_q30_rate: 3100 | ||
| after_filtering_q30_bases: 3200 | ||
| filtering_result_passed_filter_reads: 3300 | ||
| after_filtering_gc_content: 3400 | ||
| pct_surviving: 3500 | ||
| pct_adapter: 3600 | ||
|
|
||
| custom_table_header_config: | ||
| general_stats_table: | ||
| "Total length": | ||
| hidden: True | ||
| N50: | ||
| hidden: True |
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| { | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$id": "https://raw.githubusercontent.com/ebi-metagenomics/miassembler/master/assets/schema_input.json", | ||
| "title": "ebi-metagenomics/emg-viral-pipeline - params.input schema", | ||
| "description": "Schema for the file provided with params.input", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "id": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "Sample identifier", | ||
| "minLength": 3 | ||
| }, | ||
| "assembly": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.f(ast)?a(\\.gz)?$", | ||
| "errorMessage": "Assembly file in FASTA format", | ||
| "minLength": 3 | ||
| }, | ||
| "fastq_1": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.f(ast)?q\\.gz$", | ||
| "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" | ||
| }, | ||
| "fastq_2": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.f(ast)?q\\.gz$", | ||
| "errorMessage": "FastQ file for reads 2 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" | ||
| } | ||
| }, | ||
| "required": ["id"], | ||
| "oneOf": [ | ||
| { | ||
| "required": ["assembly"], | ||
| "description": "An assembly file must be provided" | ||
| }, | ||
| { | ||
| "required": ["fastq_1", "fastq_2"], | ||
| "description": "Both fastq_1 and fastq_2 files must be provided" | ||
| } | ||
| ], | ||
| "errorMessage": { | ||
| "oneOf": "You must specify either an assembly file or both fastq_1 and fastq_2 files." | ||
| } | ||
| } | ||
| } |
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|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| MGnify genomes-generation pipeline Nextflow base config file | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| A 'blank slate' config file, appropriate for general use on most high performance | ||
| compute environments. Assumes that all software is installed and available on | ||
| the PATH. Runs in `local` mode - all jobs will be run on the logged in environment. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
|
|
||
| cpus = { check_max( 1 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 6.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 4.h * task.attempt, 'time' ) } | ||
|
|
||
| errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } | ||
| maxRetries = 3 | ||
| maxErrors = '-1' | ||
|
|
||
| // Process-specific resource requirements | ||
| // NOTE - Please try and re-use the labels below as much as possible. | ||
| // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. | ||
| // If possible, it would be nice to keep the same label naming convention when | ||
| // adding in your local modules too. | ||
| // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors | ||
|
|
||
| withLabel:process_single { | ||
| cpus = { check_max( 1 , 'cpus' ) } | ||
| memory = { check_max( 6.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 4.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_low { | ||
| cpus = { check_max( 2 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 12.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 4.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_medium { | ||
| cpus = { check_max( 6 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 36.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 8.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_high { | ||
| cpus = { check_max( 12 * task.attempt, 'cpus' ) } | ||
| memory = { check_max( 72.GB * task.attempt, 'memory' ) } | ||
| time = { check_max( 16.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_long { | ||
| time = { check_max( 20.h * task.attempt, 'time' ) } | ||
| } | ||
| withLabel:process_high_memory { | ||
| memory = { check_max( 200.GB * task.attempt, 'memory' ) } | ||
| } | ||
| withLabel:error_ignore { | ||
| errorStrategy = 'ignore' | ||
| } | ||
| withLabel:error_retry { | ||
| errorStrategy = 'retry' | ||
| maxRetries = 2 | ||
| } | ||
| withName:CUSTOM_DUMPSOFTWAREVERSIONS { | ||
| cache = false | ||
| } | ||
| } |
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| process { | ||
| withNAME: ANNOTATION { conda = "$baseDir/envs/python3.yaml" } | ||
| withNAME: ASSIGN { conda = "$baseDir/envs/python3.yaml" } | ||
| withNAME: BALLOON { conda = "$baseDir/envs/balloon.yaml" } | ||
| withNAME: basics { conda = "$baseDir/envs/python3.yaml" } | ||
| withNAME: BLAST { conda = "$baseDir/envs/blast.yaml" } | ||
| withNAME: HMMSCAN { conda = "$baseDir/envs/hmmer.yaml" } | ||
| withNAME: KAIJU { conda = "$baseDir/envs/kaiju.yaml" } | ||
| withNAME: KRONA { conda = "$baseDir/envs/krona.yaml" } | ||
| withNAME: PLOT_CONTIG_MAP { conda = "$baseDir/envs/r.yaml" } | ||
| withNAME: PARSE { conda = "$baseDir/envs/python3.yaml" } | ||
| withNAME: PRODIGAL { conda = "$baseDir/envs/prodigal.yaml" } | ||
| withNAME: PHANOTATE { conda = "$baseDir/envs/phanotate.yaml" } | ||
| withNAME: python3 { conda = "$baseDir/envs/python3.yaml" } | ||
| withNAME: RATIO_EVALUE { conda = "$baseDir/envs/python3.yaml" } | ||
| withNAME: ruby { conda = "$baseDir/envs/ruby.yaml" } | ||
| withNAME: VIRSORTER { conda = "$baseDir/envs/virsorter.yaml" } | ||
| withNAME: VIRFINDER { conda = "$baseDir/envs/virfinder.yaml" } | ||
| withNAME: CHECKV { conda = "$baseDir/envs/checkv.yaml" } | ||
| } |
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| process.executor = 'local' | ||
|
|
||
| process { | ||
| withName: ANNOTATION { cpus = 1; } | ||
| withName: ASSIGN { cpus = 1; } | ||
| withName: BALLOON { cpus = 1; } | ||
| withLabel: basics { cpus = 1; } | ||
| withName: BLAST { cpus = params.cores; } | ||
| withName: CHROMOMAP { cpus = 1; } | ||
| withName: CHECKV { cpus = params.cores } | ||
| withName: FASTP { cpus = params.cores; } | ||
| withName: FASTQC { cpus = params.cores; } | ||
| withName: HMMSCAN { cpus = params.cores; } | ||
| withName: KAIJU { cpus = params.cores; } | ||
| withName: KRONA { cpus = params.cores; } | ||
| withName: PLOT_CONTIG_MAP { cpus = 1; } | ||
| withName: PPRMETA { cpus = params.cores; } | ||
| withName: MULTIQC { cpus = params.cores; } | ||
| withName: PARSE { cpus = 1; } | ||
| withName: PRODIGAL { cpus = 1; } | ||
| withName: PHANONATE { cpus = 1; } | ||
| withLabel: python3 { cpus = 1; } | ||
| withName: RATIO_EVALUE { cpus = 1; } | ||
| withLabel: ruby { cpus = 1; } | ||
| withName: SPADES { cpus = params.cores; } | ||
| withName: SANKEY { cpus = 1; } | ||
| withName: VIRSORTER { cpus = params.cores; } | ||
| withName: VIRFINDER { cpus = 1; } | ||
| withName: MASHMAP { cpus = params.cores; } | ||
| } | ||
|
|
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