Explore Workflows

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Graph Name Retrieved From View
workflow graph Cellranger Reanalyze

Cellranger Reanalyze ====================

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph hisat2-stringtie_wf_pe.cwl

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/hisat2-stringtie/paired_end/hisat2-stringtie_wf_pe.cwl

Branch/Commit ID: f85f2cd5d888ed947f47a391eb32dcb53265f9b3
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: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb
workflow graph GATK4_SomaticVariantCaller_4_1_3_0.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/GATK4_SomaticVariantCaller_4_1_3_0.cwl

Branch/Commit ID: 5ba65e4781f03a74a845b7cd40bbf4c2ae3a9844
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 8438316338e66823e1c9aca9f675b2bf33f2aa59
workflow graph heatmap-prepare.cwl

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/Barski-lab/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 2ffe30af333aead4f2a7e181ab151587e825b384
workflow graph gathered exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_gathered.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 4e2a295bb6c8b4982402ee80538a0cdb8ee6b6dd