Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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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: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a |
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workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_dispatch/workflow.cwl Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2 |
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readme-assembly-workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_create_readme/readme-assembly-workflow.cwl Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2 |
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readme-genePrediction-workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_create_readme/readme-genePrediction-workflow.cwl Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2 |
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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: d06eaa0bd48987b4975257694a32200cfc8f5bea |
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workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_download/workflow.cwl Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2 |
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RNA-Seq alignment and transcript/gene abundance workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/rnaseq.cwl Branch/Commit ID: 9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e |
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workflow.cwl
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https://github.com/NAL-i5K/Organism_Onboarding.git
Path: flow_md5checksums/workflow.cwl Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2 |
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RNASelector as a CWL workflow
https://doi.org/10.1007/s12275-011-1213-z |
https://github.com/proteinswebteam/ebi-metagenomics-cwl.git
Path: workflows/rna-selector.cwl Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193 |
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bam_filtering
BAM filtering |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_operations/subworkflows/bam_filtering.cwl Branch/Commit ID: 3f6a871f81f343cf81a345f73ff2eeac70804b8c |
