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| <body> | |
| <nav class="navbar"> | |
| <ul class="nav navbar-nav" > | |
| <li ><a href="#"><span class="glyphicon glyphicon-home dataset_name"> Research Object Crate for Metagenomics workflow</span></a></li> | |
| </ul> | |
| </nav> | |
| <div class="container"> | |
| <div class="jumbotron"> | |
| <h4 class="citation"></h3> | |
| <h3 class="item_name">Research Object Crate for Metagenomics workflow</h4> | |
| <a href="./ro-crate-metadata.json">⬇️🏷️ Download all the metadata for <span class='name'>Research Object Crate for Metagenomics workflow</span> in JSON-LD format</a> | |
| <div class="check"></div> | |
| </div> | |
| <div id="summary"> | |
| <div><h3></h3><table class="table metadata table-striped" id="./"><tbody><tr><th style="white-space: nowrap; width: 1%;">name<span> </span><a href="http://schema.org/name">[?]</a></th><td style="text-align:left"> <span>Research Object Crate for Metagenomics workflow</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">@type</th><td style="text-align:left"> <span>Dataset</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">description<span> </span><a href="http://schema.org/description">[?]</a></th><td style="text-align:left"> <span>Workflow for Metagenomics from raw reads to annotated bins. | |
| Steps: | |
| - workflow_quality.cwl: | |
| - FastQC (control) | |
| - fastp (trimming) | |
| - Kraken2 (Taxonomic Read Classification | |
| - SPAdes (Assembly) | |
| - QUAST (Assembly quality report) | |
| - BBmap (Read mapping to assembly) | |
| - sam_to_bam (sam to indexed bam) | |
| - metabatContigDepths (jgi_summarize_bam_contig_depths) | |
| - MetaBat2 (binning) | |
| </span></td></tr><tr><th style="white-space: nowrap;">Referenced by</th><td style="text-align:left"> <tbody><tr><th style="white-space: nowrap; width: 1%;">about<span> </span><a href="http://schema.org/about">[?]</a></th><td style="text-align:left"> <ul><li><a href="#ro-crate-metadata.json">ro-crate-metadata.json</a></li><li><a href="#ro-crate-preview.html">ro-crate-preview.html</a></li></ul></td></tr></tbody></td></tr><tr><th style="white-space: nowrap; width: 1%;">mainEntity<span> </span><a href="http://schema.org/mainEntity">[?]</a></th><td style="text-align:left"> <a href="#workflow_metagenomics.cwl">Metagenomics workflow</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">hasPart<span> </span><a href="http://schema.org/hasPart">[?]</a></th><td style="text-align:left"> <a href="#workflow_metagenomics.cwl">Metagenomics workflow</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">identifier<span> </span><a href="http://schema.org/identifier">[?]</a></th><td style="text-align:left"> <a href="http://localhost:3000/workflows/2?version=1">http://localhost:3000/workflows/2?version=1</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">url<span> </span><a href="http://schema.org/url">[?]</a></th><td style="text-align:left"> <a href="http://localhost:3000/workflows/2/ro_crate?version=1">http://localhost:3000/workflows/2/ro_crate?version=1</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">isBasedOn<span> </span><a href="http://schema.org/isBasedOn">[?]</a></th><td style="text-align:left"> <a href="https://git.wur.nl/unlock/cwl/-/raw/master/cwl/workflows/workflow_metagenomics.cwl">https://git.wur.nl/unlock/cwl/-/raw/master/cwl/workflows/workflow_metagenomics.cwl</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">sdDatePublished<span> </span><a href="http://schema.org/sdDatePublished">[?]</a></th><td style="text-align:left"> <span>2021-04-14 12:12:51 +0100</span></td></tr></tbody></table></div><div><h3><a href="workflow_metagenomics.cwl">⬇️ Download: workflow_metagenomics.cwl</a></h3><table class="table metadata table-striped" id="workflow_metagenomics.cwl"><tbody><tr><th style="white-space: nowrap; width: 1%;">name<span> </span><a href="http://schema.org/name">[?]</a></th><td style="text-align:left"> <span>Metagenomics workflow</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">@type</th><td style="text-align:left"> <ul><li><span>File</span></li><li><span>SoftwareSourceCode</span></li><li><span>ComputationalWorkflow</span></li></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">description<span> </span><a href="http://schema.org/description">[?]</a></th><td style="text-align:left"> <span>Workflow for Metagenomics from raw reads to annotated bins. | |
| Steps: | |
| - workflow_quality.cwl: | |
| - FastQC (control) | |
| - fastp (trimming) | |
| - Kraken2 (Taxonomic Read Classification | |
| - SPAdes (Assembly) | |
| - QUAST (Assembly quality report) | |
| - BBmap (Read mapping to assembly) | |
| - sam_to_bam (sam to indexed bam) | |
| - metabatContigDepths (jgi_summarize_bam_contig_depths) | |
| - MetaBat2 (binning) | |
| </span></td></tr><tr><th style="white-space: nowrap; width: 1%;">contentSize<span> </span><a href="http://schema.org/contentSize">[?]</a></th><td style="text-align:left"> <span>4483</span></td></tr><tr><th style="white-space: nowrap;">Referenced by</th><td style="text-align:left"> <tbody><tr><th style="white-space: nowrap; width: 1%;">mainEntity<span> </span><a href="http://schema.org/mainEntity">[?]</a></th><td style="text-align:left"> <a href="#./">Research Object Crate for Metagenomics workflow</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">hasPart<span> </span><a href="http://schema.org/hasPart">[?]</a></th><td style="text-align:left"> <a href="#./">Research Object Crate for Metagenomics workflow</a></td></tr></tbody></td></tr><tr><th style="white-space: nowrap; width: 1%;">programmingLanguage<span> </span><a href="http://schema.org/programmingLanguage">[?]</a></th><td style="text-align:left"> <a href="##cwl">Common Workflow Language</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">url<span> </span><a href="http://schema.org/url">[?]</a></th><td style="text-align:left"> <a href="https://git.wur.nl/unlock/cwl/-/raw/master/cwl/workflows/workflow_metagenomics.cwl">https://git.wur.nl/unlock/cwl/-/raw/master/cwl/workflows/workflow_metagenomics.cwl</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">keywords<span> </span><a href="http://schema.org/keywords">[?]</a></th><td style="text-align:left"> <ul></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">license<span> </span><a href="http://schema.org/license">[?]</a></th><td style="text-align:left"> <a href="https://opensource.org/licenses/CPAL-1.0">https://opensource.org/licenses/CPAL-1.0</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">creator<span> </span><a href="http://schema.org/creator">[?]</a></th><td style="text-align:left"> </td></tr><tr><th style="white-space: nowrap; width: 1%;">producer<span> </span><a href="http://schema.org/producer">[?]</a></th><td style="text-align:left"> <a href="#http://localhost:3000/projects/1">Default Project</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">dateCreated<span> </span><a href="http://schema.org/dateCreated">[?]</a></th><td style="text-align:left"> <span>[object Object]</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">dateModified<span> </span><a href="http://schema.org/dateModified">[?]</a></th><td style="text-align:left"> <span>[object Object]</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">sdPublisher<span> </span><a href="http://schema.org/sdPublisher">[?]</a></th><td style="text-align:left"> <a href="#http://localhost:3000">Alan's SEEK</a></td></tr><tr><th style="white-space: nowrap; width: 1%;">version<span> </span><a href="http://schema.org/version">[?]</a></th><td style="text-align:left"> <span>1</span></td></tr><tr><th style="white-space: nowrap; width: 1%;">input<span> </span><a href="https://bioschemas.org/ComputationalWorkflow#input">[?]</a></th><td style="text-align:left"> <ul><li><a href="##metagenomics_workflow-inputs-filter_rrna">rRNA filtering</a></li><li><a href="##metagenomics_workflow-inputs-forward_reads">forward reads</a></li><li><a href="##metagenomics_workflow-inputs-reverse_reads">reverse reads</a></li><li><a href="##metagenomics_workflow-inputs-threads">number of threads</a></li><li><a href="##metagenomics_workflow-inputs-memory">memory usage (mb)</a></li><li><a href="##metagenomics_workflow-inputs-gzip">gzip compression</a></li><li><a href="##metagenomics_workflow-inputs-kraken_database">Kraken2 database</a></li><li><a href="##metagenomics_workflow-inputs-pacbio_reads">pacbio reads</a></li></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">output<span> </span><a href="https://bioschemas.org/ComputationalWorkflow#output">[?]</a></th><td style="text-align:left"> <ul><li><a href="##metagenomics_workflow-outputs-fastqc_output">FASTQC</a></li><li><a href="##metagenomics_workflow-outputs-filter_output">Filtered reads</a></li><li><a href="##metagenomics_workflow-outputs-kraken2_output">KRAKEN2</a></li><li><a href="##metagenomics_workflow-outputs-spades_output">SPADES</a></li><li><a href="##metagenomics_workflow-outputs-quast_output">QUAST</a></li><li><a href="##metagenomics_workflow-outputs-bam_output">BAM files</a></li><li><a href="##metagenomics_workflow-outputs-metabat2_output">MetaBat2</a></li></ul></td></tr><tr><th style="white-space: nowrap; width: 1%;">dct:conformsTo</th><td style="text-align:left"> <a href="https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/">https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/</a></td></tr></tbody></table></div> | |
| </div> | |
| <p>This file was created at 1618402957840 by | |
| <a href='https://code.research.uts.edu.au/eresearch/calcytejs'> | |
| Calcyte</a> which implements the <a href=''> | |
| Draft RO-Crate format</a>, version | |
| </p> | |
| </body> | |
| </html> |
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