Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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exome alignment with qc, no bqsr, no verify_bam_id
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/pipelines/alignment_exome_mouse.cwl Branch/Commit ID: downsample_and_recall |
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04-peakcall-pe.cwl
ATAC-seq 04 quantification - PE |
https://github.com/Duke-GCB/GGR-cwl.git
Path: v1.0/ATAC-seq_pipeline/04-peakcall-pe.cwl Branch/Commit ID: v1.0.0 |
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cram_to_bam workflow
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https://github.com/genome/analysis-workflows.git
Path: cram_to_bam/workflow.cwl Branch/Commit ID: toil_compatibility |
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wf_get_peaks_scatter_se_nostats.cwl
The \"main\" workflow. Takes fastq files generated using the seCLIP protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/) and outputs candidate RBP binding regions (peaks). runs: wf_get_peaks_se.cwl through scatter across multiple samples. |
https://github.com/YeoLab/eclip.git
Path: cwl/wf_get_peaks_scatter_se_nostats.cwl Branch/Commit ID: master |
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download_fastq.cwl
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https://github.com/uc-cdis/genomel_pipelines.git
Path: genomel/cwl/workflows/utils/download_fastq.cwl Branch/Commit ID: master |
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prefetch_fastq.cwl
Worfklow combining an SRA fetch from NCBI with a fastq-dump cmd |
https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git
Path: bio-cwl-tools/sratoolkit/prefetch_fastq.cwl Branch/Commit ID: master |
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WGS and MT analysis for fastq files
rna / protein - qc, preprocess, filter, annotation, index, abundance |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/wgs-fastq.workflow.cwl Branch/Commit ID: master |
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Functional analyis of sequences that match the 16S SSU
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/16S_taxonomic_analysis.cwl Branch/Commit ID: 1b0851e |
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Quality assessment, amplicon classification and functional prediction
Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_ngtax_picrust2.cwl Branch/Commit ID: master |
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pipeline_v2.cwl#openoil_pipeline
Animation of an oil spill with openoil |
https://github.com/ILIAD-ocean-twin/application_package.git
Path: openoil/pipeline_v2.cwl Branch/Commit ID: main Packed ID: openoil_pipeline |