Explore Workflows

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

Graph Name Retrieved From View
workflow graph 03-map-pe-blacklist-removal.cwl

ATAC-seq 03 mapping - reads: PE - blacklist removal

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

Path: v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl

Branch/Commit ID: master
workflow graph waltz-workflow.cwl

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

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: master
workflow graph workflow-pepinfo-backtranseq-cpgplot.cwl

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-pepinfo-backtranseq-cpgplot.cwl

Branch/Commit ID: master
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: No_filters_detect_variants
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: master
workflow graph completeWorkflow.cwl

https://github.com/h3abionet/h3abionet16S.git

Path: workflows-cwl/completeWorkflow.cwl

Branch/Commit ID: master
workflow graph somatic_exome: exome alignment and somatic variant detection

somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: low-vaf
workflow graph Detect Variants workflow for WGS pipeline

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: low-vaf
workflow graph retrieve sequence and perform pairwise alignment (sub-workflow process)

\"Perform pairwise alignment of protein sequences for pairs identified by structural similarity search. Step 1: retrieve sequence from blastdbcmd result Step 2: makeblastdb: ../Tools/14_makeblastdb.cwl Step 3: blastdbcmd: ../Tools/15_blastdbcmd.cwl Step 4: seqretsplit: ../Tools/16_seqretsplit.cwl Step 5: needle (Global alignment): ../Tools/17_needle.cwl Step 6: water (Local alignment): ../Tools/17_water.cwl\"

https://github.com/yonesora56/plant2human.git

Path: Workflow/11_retrieve_sequence_wf.cwl

Branch/Commit ID: main
workflow graph SSU-from-tablehits.cwl

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 3f85843