Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph bam to trimmed fastqs and HISAT alignments

https://github.com/fgomez02/analysis-workflows.git

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: No_filters_detect_variants
workflow graph snp_callers_workflow.cwl

A workflow for running MuSe, MuTect, SomaticSniper, and Pindel. See [the github repository](https://github.com/BD2KGenomics/dockstore_workflow_snps) for details.

https://github.com/BD2KGenomics/dockstore_workflow_snps.git

Path: snp_callers_workflow.cwl

Branch/Commit ID: master
workflow graph Exome QC workflow

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: downsample_and_recall
workflow graph kfdrc_cram_to_gvcf.cwl

https://github.com/cr-ste-justine/chujs-alignment-workflow.git

Path: workflows/kfdrc_cram_to_gvcf.cwl

Branch/Commit ID: dev
workflow graph Functional analyis of sequences that match the 16S SSU

https://github.com/farahzkhan/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: master
workflow graph wf_self_consistency_ratio.cwl

Computes the self-consistency ratio (see Gabe's protocols paper, or CHIP SEQ). Given two replicates, split each and perform IDR on each fragment. Returns the ratio of max(N1, N2)/min(N1, N2) where N1, N2 are the numbers of reproducible peaks found between each rep split pair.

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_self_consistency_ratio.cwl

Branch/Commit ID: master
workflow graph wf_trim_and_map_se.cwl

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/YeoLab/eclip.git

Path: cwl/wf_trim_and_map_se.cwl

Branch/Commit ID: master
workflow graph predixcan.cwl

https://github.com/cwl-apps/predixcan_tools.git

Path: predixcan/predixcan.cwl

Branch/Commit ID: main
workflow graph 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
workflow graph repliseq-parta.cwl

https://github.com/mr-c/4dn-dcic-pipelines-cwl.git

Path: cwl_awsem_v1/repliseq/repliseq-parta.cwl

Branch/Commit ID: master