Explore Workflows

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

Graph Name Retrieved From View
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph Cell Ranger Aggregate (RNA, RNA+VDJ)

Cell Ranger Aggregate (RNA, RNA+VDJ) Combines outputs from multiple runs of either “Cell Ranger Count (RNA)” or “Cell Ranger Count (RNA+VDJ)” pipelines. The results of this workflow are primarily used in “Single-Cell RNA-Seq Filtering Analysis” and “Single-Cell Immune Profiling Analysis” pipelines.

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

Path: workflows/cellranger-aggr.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph Single-Cell Multiome ATAC-Seq and RNA-Seq Filtering Analysis

Single-Cell Multiome ATAC-Seq and RNA-Seq Filtering Analysis Removes low-quality cells from the outputs of the “Cell Ranger Count (RNA+ATAC)” and “Cell Ranger Aggregate (RNA+ATAC)” pipelines. The results of this workflow are used in the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” and “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipelines.

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

Path: workflows/sc-multiome-filter.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph kfdrc_process_se_set.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: subworkflows/kfdrc_process_se_set.cwl

Branch/Commit ID: 47e3dadcbdb6a07acaf74cdfb91554aabe5e4b24
workflow graph taxcheck.cwl

Perform taxonomic identification tasks on an input genome

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

Path: taxcheck.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: ead263db0e167db39ddbdc79b04d343943d129b6
workflow graph Build Bowtie indices

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome

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

Path: workflows/bowtie-index.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f
workflow graph Feature expression merge - combines feature expression from several experiments

Feature expression merge - combines feature expression from several experiments ========================================================================= Workflows merges RPKM (by default) gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns (by default). Reported unique columns are renamed based on the experiments names.

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

Path: workflows/feature-merge.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/revsort.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph Interval overlapping alignments counts

Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals.

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

Path: workflows/bedtools-multicov.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa