Explore Workflows

This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/standard_pipeline.cwl

Branch/Commit ID: master

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/chksum_for_a_corrupted_xam_file.cwl

Branch/Commit ID: master

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/BQSR/bqsr_workflow.cwl

Branch/Commit ID: 0.0.33_dmp

QIIME2 Deblur, feature summaries, phylogenetic diversity tree, taxonomic analysis and ancom

https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step2-deblur.cwl

Branch/Commit ID: qiime2-workflow

Packed ID: main

The BD Rhapsody™ WTA Analysis Pipeline is used to create sequencing libraries from single cell transcriptomes without having to specify a targeted panel. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file and a transcriptome annotation file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file.

https://github.com/aheinzel/tmp_rhapsody_for_cwl_vis.git

Path: wf.cwl

Branch/Commit ID: main

Packed ID: main

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

Path: workflows/GATK/GATK-Sub-Workflow-h3abionet-snp.cwl

Branch/Commit ID: h3abionet-gatk-workflow

https://github.com/hamid58b/cancer-genomics-workflow.git

Path: varscan/bgzip_and_index.cwl

Branch/Commit ID: master

https://doi.org/10.1007/s12275-011-1213-z

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

Path: workflows/rna-selector.cwl

Branch/Commit ID: 8515542

https://gitlab.ebrains.eu/sofiakar/yre-standardised-workflows.git

Path: Workflows/PSD_workflow_bucket_1/workflow.cwl

Branch/Commit ID: main

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/chksum_seqval_wf_interleaved_fq.cwl

Branch/Commit ID: v0.1.0