Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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predixcan.cwl
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https://github.com/cwl-apps/predixcan_tools.git
Path: predixcan/predixcan.cwl Branch/Commit ID: main |
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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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repliseq-parta.cwl
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https://github.com/mr-c/4dn-dcic-pipelines-cwl.git
Path: cwl_awsem_v1/repliseq/repliseq-parta.cwl Branch/Commit ID: master |
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Replace legacy AML Trio Assay
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https://github.com/apaul7/cancer-genomics-workflow.git
Path: definitions/pipelines/aml_trio_cle.cwl Branch/Commit ID: low-vaf |
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CNV_pipeline
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/workflow.cwl Branch/Commit ID: 1.0.5 |
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qiime2 create feature visual summaries
FeatureTable and FeatureData summaries from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
https://github.com/duke-gcb/bespin-cwl.git
Path: packed/qiime2-step2-dada2.cwl Branch/Commit ID: qiime2-workflow Packed ID: qiime2-04-features.cwl |
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EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.
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https://github.com/farahzkhan/ebi-metagenomics-cwl.git
Path: workflows/emg-qc-single.cwl Branch/Commit ID: master |
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anonymize.cwl
Replace named entities in a directory of text files. Can be used as part of an data anonymization workflow. |
https://github.com/WhatWorksWhenForWhom/nlppln.git
Path: nlppln/cwl/anonymize.cwl Branch/Commit ID: master |
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qiime2 demux sequences
Demultiplexing sequences from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/ |
https://github.com/Duke-GCB/bespin-cwl.git
Path: packed/qiime2-step1-import-demux.cwl Branch/Commit ID: qiime2-workflow Packed ID: qiime2-02-demux.cwl |
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HS Metrics workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/hs_metrics.cwl Branch/Commit ID: master |
