Explore Workflows

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Graph Name Retrieved From View
workflow graph atm-plev.cwl

https://github.com/E3SM-Project/e3sm_to_cmip.git

Path: scripts/cwl_workflows/atm-mon-plev/atm-plev.cwl

Branch/Commit ID: cee5c228f6085b0afd4a4c4696f0c947b1514f50
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
workflow graph Bismark Methylation - pipeline for BS-Seq data analysis

Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).

 https://github.com/datirium/workflows.git

Path: workflows/bismark-methylation-se.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
workflow graph workflow.cwl

https://github.com/vavien/bi-cwl.git

Path: workflow.cwl

Branch/Commit ID: d40663cb07f9f0f700ddd1578f9a895dd8432070
workflow graph worldpopulation.cwl

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation.cwl

Branch/Commit ID: 379334455b663b295a61a0ec057bfc080f9c7c6e
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 7ebb8d2757914d16520b00571a281e2ad86a42cf
workflow graph STAR-RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq_star_fusion.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
workflow graph bacterial_orthology

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

Path: bacterial_orthology/wf_bacterial_orthology.cwl

Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: ec5355f335852e51c6938809c16ea1d230a3f983