Explore Workflows

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Graph Name Retrieved From View
workflow graph Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

https://github.com/ncbi/pgap.git

Path: bacterial_annot/wf_bacterial_annot_pass3.cwl

Branch/Commit ID: 13b411d94a568e52797ba936732dc65f1a91bd41
workflow graph count-lines1-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 2a922ab11b2f9c21ae4955c74563543b87717b93
workflow graph allele-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

https://github.com/Barski-lab/workflows.git

Path: subworkflows/allele-alignreads-se-pe.cwl

Branch/Commit ID: 69a15832fae36a128b6cbf74187dac0dd9cfae27
workflow graph xenbase-sra-to-fastq-pe.cwl

https://github.com/Barski-lab/workflows.git

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: 69a15832fae36a128b6cbf74187dac0dd9cfae27
workflow graph Varscan Workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
workflow graph kmer_cache_store

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 4cd1fb565519fbe5f9c462acae01ff608c3784a3
workflow graph taxonomy_check_16S

https://github.com/ncbi/pgap.git

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 7e3e1cb249e85285e27ef3ebd4104965f835241d
workflow graph gsmcal.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_target/gsmcal.cwl

Branch/Commit ID: b139045507381d9fdaad02d719c7b9bfe809fec8
workflow graph wgs alignment and germline variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: 1585504ccffafac53b1594349ed934f45206ee2b
workflow graph kmer_build_tree

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 3bec7182e39cb4af10ed8920639adfa78a28ed81