Explore Workflows

Generates tag density heatmap and histogram for the centered list of features in a headerless regions file. - If provided regions file is a gene list with the following columns `chrom start end name score strand` set `Gene TSS` as a re-centering criteria. - If provided regions file is a peak list with the following columns `chrom start end name` set `Peak Center` as a re-centering criteria. `score` column is always ignored.

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

Path: workflows/heatmap.cwl

Branch/Commit ID: 46d3d403ddb240d5a8f4f31ab992b6d6a2686745

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: ffab5424bb8b5905aecf6f8e2e6387da7f3df562

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

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

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 4a80f5b8f86c83af39494ecc309b789aeda77964

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: 7eef0294395d83ff0765fce61726a59d71126422

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/env-wf3.cwl

Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c

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

Path: progs/protein_extract.cwl

Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines5-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621