Explore Workflows

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

Graph Name Retrieved From View
workflow graph 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: a839eb6390974089e1a558c49fc07b4c66c50767
workflow graph Filter differentially expressed genes from DESeq for Tag Density Profile Analyses

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

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

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: a8eaf61c809d76f55780b14f2febeb363cf6373f
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: ce6b6948f82a7d521b9f11c2d9dc73e3b009ebbe
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d
workflow graph WGS processing workflow for single sample

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl

Branch/Commit ID: d147d1d1fafeeea06bd09d9479337b0f5aab43b0
workflow graph Downsample and HaplotypeCaller

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

Path: definitions/pipelines/downsample_and_recall.cwl

Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325