Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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default-wf5.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/default-wf5.cwl Branch/Commit ID: 20f01e04328537714e57d136e242d3e7a9d44266 |
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wgs alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/alignment_wgs.cwl Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46 |
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fp_filter workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/fp_filter.cwl Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46 |
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wgs alignment and germline variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_wgs.cwl Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46 |
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maf2vcf_gz_workflow.cwl
Workflow to convert a maf file into a vcf.gz with .tbi index |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/maf2vcf_gz_workflow.cwl Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933 |
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example.cwl
Example CWL workflow that uses some advanced features |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/example.cwl Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933 |
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Trim Galore RNA-Seq pipeline paired-end
The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file |
https://github.com/datirium/workflows.git
Path: workflows/trim-rnaseq-pe.cwl Branch/Commit ID: 5e7385b8cfa4ddae822fff37b6bd22eb0370b389 |
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Cellranger reanalyze - reruns secondary analysis performed on the feature-barcode matrix
Devel version of Single-Cell Cell Ranger Reanalyze ================================================== Workflow calls \"cellranger aggr\" command to rerun secondary analysis performed on the feature-barcode matrix (dimensionality reduction, clustering and visualization) using different parameter settings. As an input we use filtered feature-barcode matrices in HDF5 format from cellranger count or aggr experiments. Note, we don't pass aggregation_metadata from the upstream cellranger aggr step. Need to address this issue when needed. |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-reanalyze.cwl Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b |
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count-lines11-wf-noET.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines11-wf-noET.cwl Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3 |
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chipseq-gen-bigwig.cwl
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https://github.com/datirium/workflows.git
Path: subworkflows/chipseq-gen-bigwig.cwl Branch/Commit ID: 01c6af7a598eb44f6bcaa9b5eecf13229f28546e |
