Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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Hello World
Outputs a message using echo |
https://gitlab.cs.man.ac.uk/soiland-reyes/test1337.git
Path: hello.cwl Branch/Commit ID: master |
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metabarcode (gene amplicon) analysis for fastq files
protein - qc, preprocess, annotation, index, abundance |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/metabarcode-fastq.workflow.cwl Branch/Commit ID: master |
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pindel parallel workflow
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/pindel.cwl Branch/Commit ID: downsample_and_recall |
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Illumina read quality control, trimming and contamination filter.
**Workflow for Illumina paired read quality control, trimming and filtering.**<br /> Multiple paired datasets will be merged into single paired dataset.<br /> Summary: - FastQC on raw data files<br /> - fastp for read quality trimming<br /> - BBduk for phiX and (optional) rRNA filtering<br /> - Kraken2 for taxonomic classification of reads (optional)<br /> - BBmap for (contamination) filtering using given references (optional)<br /> - FastQC on filtered (merged) data<br /> **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_illumina_quality.cwl Branch/Commit ID: master |
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transcriptome_assemble.cwl
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https://github.com/yyoshiaki/DAT2-cwl.git
Path: workflow/transcriptome_assemble/transcriptome_assemble.cwl Branch/Commit ID: develop |
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hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather
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https://github.com/ncbi/pgap.git
Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl Branch/Commit ID: test |
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chksum_seqval_wf_paired_fq.cwl
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https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_seqval_wf_paired_fq.cwl Branch/Commit ID: 0.2.2 |
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qiime2 rarefaction visualization
Alpha rarefaction plotting from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
https://github.com/bespin-workflows/16s-qiime2.git
Path: subworkflows/qiime2-07-alpha-rarefaction.cwl Branch/Commit ID: develop |
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ValidateArrayElementCoordinates
Plot and compare array element coordinates. Validate coordinate transformation from those used in observatory database to simulation systems. |
https://github.com/gammasim/workflows.git
Path: workflows/ValidateArrayElementCoordinates.cwl Branch/Commit ID: main |
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QIIME2 Step 2 (DADA2 option)
QIIME2 DADA2, feature summaries, phylogenetic diversity tree, taxonomic analysis and ancom |
https://github.com/bespin-workflows/16s-qiime2.git
Path: 16s-step2-dada2-paired.cwl Branch/Commit ID: develop |