Explore Workflows

Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files

https://github.com/mskcc/pluto-cwl.git

Path: cwl/igv-report_maf_workflow.cwl

Branch/Commit ID: 7eb2b0a4d37018142233d770595ac2e00376dab4

Wrapper to run indexing on all bams before submitting for samples fillout Includes secondary input channels to allow for including .bam files that do not have indexes Also include other extra handling needed for files that might not meet needs for the fillout workflow NOTE: need v1.1 upgrade so we can do it all from a single channel with optional secondary files; https://www.commonwl.org/v1.1/CommandLineTool.html#SecondaryFileSchema

https://github.com/mskcc/pluto-cwl.git

Path: cwl/samples_fillout_index_workflow.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

https://github.com/datirium/workflows.git

Path: workflows/super-enhancer.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd

Example CWL workflow that uses some advanced features

https://github.com/mskcc/pluto-cwl.git

Path: cwl/example_workflow.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

https://github.com/datirium/workflows.git

Path: workflows/fastqc.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

https://github.com/datirium/workflows.git

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/detect_variants_wgs_nonhuman.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2

https://github.com/ncbi/pgap.git

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 76a9637a06e2102645eae29aff10b6f7185892a5