Explore Workflows
View already parsed workflows here or click here to add your own
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lhcbreconstruct.cwl
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https://github.com/aldbr/dirac-cwl-proto.git
Path: test/workflows/lhcb/lhcbreconstruct.cwl Branch/Commit ID: 7871a462d30ddafc89b6fedcea965b9157fa7713 |
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CLE gold vcf evaluation workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/vcf_eval_cle_gold.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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chksum_for_a_corrupted_fastq_file.cwl
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https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_for_a_corrupted_fastq_file.cwl Branch/Commit ID: 0b1274e5c3a0a70dc989ac6463f7a6db5cf563c1 |
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trim-rnaseq-pe.cwl
Runs RNA-Seq BioWardrobe basic analysis with pair-end data file. |
https://github.com/Barski-lab/workflows.git
Path: workflows/trim-rnaseq-pe.cwl Branch/Commit ID: 64e85970dbecba89c3380ab285c108d221e76fe6 |
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extract_gencoll_ids
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https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 0bc1c33a2293e054ad00974971edc79c13252cc7 |
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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: 89082ba8d398033dee84c37a84c6547466c1f2d2 |
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Subworkflow to allow calling different SV callers which require bam files as inputs
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https://github.com/apaul7/cancer-genomics-workflow.git
Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d |
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Genomic regions intersection and visualization
Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them |
https://github.com/datirium/workflows.git
Path: workflows/intervene.cwl Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e |
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kmer_ref_compare_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_ref_compare_wnode.cwl Branch/Commit ID: 0bc1c33a2293e054ad00974971edc79c13252cc7 |
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LHCb MC workflow
This workflow is composed of 2 main steps that should generate 2 types of jobs: * MCSimulation (CommandLineTool): Gauss execution * MCReconstruction (Workflow): Boole, Moore, Brunel and DaVinci executions based on Gauss outputs |
https://github.com/aldbr/dirac-cwl-proto.git
Path: test/workflows/lhcb/description.cwl Branch/Commit ID: 7871a462d30ddafc89b6fedcea965b9157fa7713 |
