Explore Workflows

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

Graph Name Retrieved From View
workflow graph EMG assembly for paired end Illumina

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-assembly.cwl

Branch/Commit ID: 3f85843
workflow graph multiome pipeline using Salmon and Alevin (HuBMAP scRNA-seq pipeline) and HuBMAP scATAC-seq pipeline

https://github.com/hubmapconsortium/multiome-rna-atac-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: a33bc8a
workflow graph wf_clipseqcore_pe_2barcodes.cwl

Workflow for handling reads containing two barcodes. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs

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

Path: cwl/wf_clipseqcore_pe_2barcodes.cwl

Branch/Commit ID: master
workflow graph Mosaics two or more Landsat-8 acquisitions (includes pan-sharpening)

Mosaics two or more Landsat-8 acquisitions (includes pan-sharpening)

 https://github.com/cwl-for-eo/otb.git

Path: landsat-8-mosaic/mosaic.cwl

Branch/Commit ID: master

Packed ID: main
workflow graph qiime2 create phylogenetic tree

Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

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

Path: packed/qiime2-step2-dada2-paired.cwl

Branch/Commit ID: qiime2-workflow-paired

Packed ID: qiime2-05-phylogeny.cwl
workflow graph inp_update_wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/inp_update_wf.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.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_illumina_quality.cwl

Branch/Commit ID: master
workflow graph module-1

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/module-1.cwl

Branch/Commit ID: dev
workflow graph bulk scRNA-seq pipeline using Salmon

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: bulk-pipeline.cwl

Branch/Commit ID: main
workflow graph cmsearch-multimodel.cwl

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

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: c1f8b22