Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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gcaccess_from_list
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https://github.com/ncbi/pgap.git
Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 6fad27f92dd604eca0e341178f594a560d70953b |
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Nanopore read quality filter.
Workflow for nanopore read quality control and contamination filtering. Steps: - FastQC before filtering (read quality control) - Kraken2 taxonomic read classification - Minimap2 contamination filter based on given references - FastQC after filtering (read quality control) |
https://git.wur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_nanopore_quality.cwl Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae |
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Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass3.cwl Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8 |
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exome alignment and somatic variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/somatic_exome_nonhuman.cwl Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370 |
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Metagenomic binning from assembly
Workflow for Metagenomics from raw reads to annotated bins. Steps: - MetaBAT2 (binning) - CheckM (bin completeness and contamination) - GTDB-Tk (bin taxonomic classification) - BUSCO (bin completeness) |
https://git.wur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_metagenomics_binning.cwl Branch/Commit ID: cd0c19d51068c5407cd70b718a561d4662819d87 |
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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: 6fad27f92dd604eca0e341178f594a560d70953b |
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hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather
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https://github.com/ncbi/pgap.git
Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8 |
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samtools_sort
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_operations/subworkflows/samtools_sort.cwl Branch/Commit ID: 26ae4914651d5b3e188028d1e9d88a391b3f6730 |
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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: 480e99a4bb3046e0565113d9dca294e0895d3b0c |
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bwa_mem
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_operations/subworkflows/bwa_mem.cwl Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c |
