Explore Workflows

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

Graph Name Retrieved From View
workflow graph samples_fillout_index_batch_workflow.cwl

Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files NOTE: each sample in a sample_group must have a .bam file, and there must be a minumum of 1 .maf file amoungst samples in the same sample_group this means that for each sample in the sample_group, a .bam is required but a .maf is optional as long as one sample in the group has a .maf this also means that singleton sample groups, or a sample group with only one sample, MUST include a .maf file; singletons cannot lack a .maf NOTE: all .maf files must be valid, at a minimum they must have a header and at least one variant if a sample has no variants in its .maf file, or has an empty .maf file, then it should NOT have a maf_file entry associated with it

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

Path: cwl/samples_fillout_index_batch_workflow.cwl

Branch/Commit ID: master
workflow graph grep-and-count.cwl

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

Path: workflows/presentation-demo/grep-and-count.cwl

Branch/Commit ID: master
workflow graph 01-qc-pe.cwl

ATAC-seq 01 QC - reads: PE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/01-qc-pe.cwl

Branch/Commit ID: master
workflow graph RNASelector as a CWL workflow

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: 56dafa4
workflow graph call_cnv.cwl

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

Path: workflows/subworkflows/call_cnv.cwl

Branch/Commit ID: master
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 86fbeb95ef85111f3b4c6bc2bba8f06cef64e157
workflow graph sequence (bam or fastqs) to trimmed fastqs

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

Path: definitions/subworkflows/sequence_to_trimmed_fastq.cwl

Branch/Commit ID: master
workflow graph CODEX analysis pipeline using Cytokit

https://github.com/hubmapconsortium/codex-pipeline.git

Path: steps/ometiff_second_stitching.cwl

Branch/Commit ID: 1c73942
workflow graph EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.

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

Path: workflows/emg-qc-paired.cwl

Branch/Commit ID: 8515542
workflow graph Hello World

Outputs a message using echo

 https://gitlab.cs.man.ac.uk/soiland-reyes/test1337.git

Path: hello.cwl

Branch/Commit ID: master