Explore Workflows
View already parsed workflows here or click here to add your own
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step_valuefrom5_wf_with_id_v1_1.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/step_valuefrom5_wf_with_id_v1_1.cwl Branch/Commit ID: 33a706bc6b85f1c2824af05bebe7aae19bcb6597 |
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trim-rnaseq-pe-dutp.cwl
Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file. |
https://github.com/Barski-lab/workflows.git
Path: workflows/trim-rnaseq-pe-dutp.cwl Branch/Commit ID: a8e4c1245950715d2e07682d3ac4865ce1d73777 |
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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: a8e4c1245950715d2e07682d3ac4865ce1d73777 |
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Align reference proteins plane complete workflow
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https://github.com/ncbi/pgap.git
Path: protein_alignment/wf_protein_alignment.cwl Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5 |
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Filter Protein Seeds; Find ProSplign Alignments
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https://github.com/ncbi/pgap.git
Path: protein_alignment/wf_compart_filter_prosplign.cwl Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5 |
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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: 369e2b6c7f4db75099d258729dec1326f55d2cc5 |
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Create Genomic Collection for Bacterial Pipeline, ASN.1 input
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https://github.com/ncbi/pgap.git
Path: genomic_source/wf_genomic_source_asn.cwl Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5 |
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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: 369e2b6c7f4db75099d258729dec1326f55d2cc5 |
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trnascan_wnode and gpx_qdump combined
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https://github.com/ncbi/pgap.git
Path: bacterial_trna/wf_scan_and_dump.cwl Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5 |
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cluster_blastp_wnode and gpx_qdump combined
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https://github.com/ncbi/pgap.git
Path: task_types/tt_cluster_and_qdump.cwl Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5 |
