Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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dynresreq-workflow.cwl
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https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/dynresreq-workflow.cwl Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3 |
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bact_get_kmer_reference
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https://github.com/ncbi/pgap.git
Path: task_types/tt_bact_get_kmer_reference.cwl Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa |
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blastp_wnode_struct
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastp_wnode_struct.cwl Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71 |
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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: a8eaf61c809d76f55780b14f2febeb363cf6373f |
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Cut-n-Run pipeline paired-end
Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed |
https://github.com/datirium/workflows.git
Path: workflows/trim-chipseq-pe-cut-n-run.cwl Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c |
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SoupX Estimate
SoupX Estimate ============== |
https://github.com/datirium/workflows.git
Path: workflows/soupx.cwl Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c |
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Build Bismark indices
Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input. |
https://github.com/datirium/workflows.git
Path: workflows/bismark-index.cwl Branch/Commit ID: 7fb8a1ebf8145791440bc2fed9c5f2d78a19d04c |
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tt_fscr_calls_pass1
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https://github.com/ncbi/pgap.git
Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71 |
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final_filtering
Final filtering |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/final_filtering.cwl Branch/Commit ID: 32a040f94e9798bf91858da51598f0d68c35797d |
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samtools_sort
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/samtools_sort.cwl Branch/Commit ID: 32a040f94e9798bf91858da51598f0d68c35797d |
