Explore Workflows
View already parsed workflows here or click here to add your own
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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: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5 |
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beast-2step-workflow.cwl
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https://github.com/GusEllerm/CWL_workflows.git
Path: workflows/BEAST_examples/beast-2step-workflow.cwl Branch/Commit ID: 2c9b239c9a6278303c68357763bc9481a2ac1a3f |
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Alignment without BQSR
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022 |
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SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs. |
https://github.com/datirium/workflows.git
Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5 |
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Vcf concordance evaluation workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/vcf_eval_concordance.cwl Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f |
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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: f1eb0f4eaaf1661044f28d859f7e8d4302525ead |
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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/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5 |
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Subworkflow to allow calling different SV callers which require bam files as inputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: 2979b565f88ceebca934611adbf3fb8cefd65a19 |
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count-lines9-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines9-wf.cwl Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3 |
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genomics-workspace-protein.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_genomicsWorkspace/genomics-workspace-protein.cwl Branch/Commit ID: 0b58c250e8ab7c5efae29443f08ea74316127041 |
