Explore Workflows

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

Path: testdata/workflow_input_sf_expr_array_v1_1.cwl

Branch/Commit ID: 70fbcd9776071edc2fd884308b016a4901b97554

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

Path: tests/wf/optional_src_mandatory_sink.cwl

Branch/Commit ID: 6c86caa0571fd186d90a6600e0bb405596d4a5e0

Outputs a message using echo

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

Path: tests/wf/hello-workflow.cwl

Branch/Commit ID: 6c86caa0571fd186d90a6600e0bb405596d4a5e0

https://github.com/genome/arvados_trial.git

Path: qc/workflow_wgs.cwl

Branch/Commit ID: 202b43b7449485a317c857d62ca7d39196764e65

Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.

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

Path: tests/wf/mpi_simple_wf.cwl

Branch/Commit ID: 12993a6eb60f5ccb4edbe77cb6de661cfc496090

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

https://github.com/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: c82a2e766abba032f0bbe2aa76e0176e69064569

https://github.com/ncbi/pgap.git

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: e668f9c4047f1971ae53040a5af3eccc4bfc3c53

Workflow to convert a maf file into a vcf.gz with .tbi index

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

Path: cwl/maf2vcf_gz_workflow.cwl

Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: e668f9c4047f1971ae53040a5af3eccc4bfc3c53