Explore Workflows
View already parsed workflows here or click here to add your own
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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: af468ae34c82dc88399aeedfd8f12f1e87052367 |
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Prepare user input
Prepare user input for NCBI-PGAP pipeline |
https://github.com/ncbi/pgap.git
Path: prepare_user_input2.cwl Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b |
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contaminant_cleanup
This workflow detect and remove contamination from a DNA fasta file |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/Contamination/contaminant-cleanup.cwl Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49 |
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Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass1.cwl Branch/Commit ID: af468ae34c82dc88399aeedfd8f12f1e87052367 |
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blastp_wnode_naming
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastp_wnode_naming.cwl Branch/Commit ID: 2d851682ba1bf2aaaacb3677253b55ceb59c8568 |
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tt_kmer_compare_wnode
Pairwise comparison |
https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_compare_wnode.cwl Branch/Commit ID: 2d851682ba1bf2aaaacb3677253b55ceb59c8568 |
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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: af468ae34c82dc88399aeedfd8f12f1e87052367 |
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Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass2.cwl Branch/Commit ID: af468ae34c82dc88399aeedfd8f12f1e87052367 |
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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: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b |
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Unaligned BAM to BQSR and VCF
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl Branch/Commit ID: 1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68 |
