Explore Workflows

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Graph Name Retrieved From View
workflow graph Filter Protein Seeds; Find ProSplign Alignments

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: 41d14ec5e2dfa0fac7eebeefda1f26ccea14c9a0
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: 295e7b7f51727c0f2d6cc86ce817449b2e8dba3c
workflow graph bulk scRNA-seq pipeline using Salmon

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: bulk-pipeline.cwl

Branch/Commit ID: c01ba083d8467df40f3b87a86712a3965111d90e
workflow graph scatter-wf4.cwl#main

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-wf4.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3

Packed ID: main
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/wgs_alignment.cwl

Branch/Commit ID: 1249b5d4e23d57ca5e3b8ad6d8e5f10ddb019f68
workflow graph steplevel-resreq.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/steplevel-resreq.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
workflow graph kmer_compare_wnode

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: f18c1dce463509170ee3bf2844d5a3637ff706f5
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: 5f4f9c63a4183eabd10e11d9e86cf054ef7ced05
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/alignment_exome_nonhuman.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a