Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
Cell Ranger Count (RNA)
Cell Ranger Count (RNA) Quantifies single-cell gene expression of the sequencing data from a single 10x Genomics library. The results of this workflow are primarily used in either “Single-Cell RNA-Seq Filtering Analysis” or “Cell Ranger Aggregate (RNA, RNA+VDJ)” pipelines. |
https://github.com/datirium/workflows.git
Path: workflows/single-cell-preprocess-cellranger.cwl Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908 |
|
|
|
blastp_wnode_naming
|
https://github.com/ncbi/pgap.git
Path: task_types/tt_blastp_wnode_naming.cwl Branch/Commit ID: 5b498b4c4f17bb8f17e6886aa4c5661d7aba34fc |
|
|
|
Pairwise genomic regions intersection
Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments |
https://github.com/datirium/workflows.git
Path: workflows/peak-intersect.cwl Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908 |
|
|
|
tld.cwl
|
https://github.com/simleo/workflow-run-crate.git
Path: tools/cwlprov_to_crate/tld/tld.cwl Branch/Commit ID: ac186731ff21005fa908d2d3a9426034e3c367b3 |
|
|
|
bam-bedgraph-bigwig.cwl
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: 896422c9ff1995024cb77675edcd4d973ae11f7a |
|
|
|
Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)
|
https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass1.cwl Branch/Commit ID: 1cfd46014be8d867044cb10d1ddde0cb3068ee84 |
|
|
|
bam-bedgraph-bigwig.cwl
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/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726 |
|
|
|
trnascan_wnode and gpx_qdump combined
|
https://github.com/ncbi/pgap.git
Path: bacterial_trna/wf_scan_and_dump.cwl Branch/Commit ID: 1cfd46014be8d867044cb10d1ddde0cb3068ee84 |
|
|
|
extract_gencoll_ids
|
https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 4ffbad9ffeab15ec8af5f6f91bd352ef96d1ef77 |
|
|
|
checkm
|
https://github.com/ncbi/pgap.git
Path: checkm/wf_checkm.cwl Branch/Commit ID: 4ffbad9ffeab15ec8af5f6f91bd352ef96d1ef77 |
