Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Aligning chipseq data of mouse

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

Path: definitions/subworkflows/sequence_to_bqsr_mouse.cwl

Branch/Commit ID: 3b6d0475c80f5e452793a46a38ee188742b86595
workflow graph workflow.cwl

https://github.com/imilos/silicofcm-workflows.git

Path: ultrasound-height-parametric/workflow.cwl

Branch/Commit ID: 92d00c0d6fd5d462606bbaf0a8a9fc039d3d2c83
workflow graph QIIME2 Step 1 paired end sequences

QIIME2 Import and Demux Step 1 paired end sequences

https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step1-import-demux-paired.cwl

Branch/Commit ID: ef08cb00bd55b4c712645d171dbc691e01ed6165

Packed ID: main
workflow graph default-wf5.cwl

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: bc0f1f147231c759fb2d5ff99f41b2667a5588ad
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: ece70ac30cd87100a70f7dc64d08fa72724e9416
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: b12ec8c8e832151033b9e6c0a76a3c3df18d45da
workflow graph deconv-cor-single-mat.cwl

https://github.com/PNNL-CompBio/decomprolute.git

Path: metrics/mrna-prot/deconv-cor-single-mat.cwl

Branch/Commit ID: 010b416623cd217a6300f96cc0623bc8fde690d9
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: 46a077b51619c6a14f85e0aa5260ae8a04426fab
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 33dcc054a8718edad26440f085d73b7c5d7b7871