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Graph Name Retrieved From View
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: 17a4a68b20e0af656e09714c1f39fe761b518686
workflow graph pipeline-se.cwl

ATAC-seq pipeline - reads: SE

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

Path: v1.0/ATAC-seq_pipeline/pipeline-se.cwl

Branch/Commit ID: 8d02684ae0ff27e641f3704686e3bc8b1979b854
workflow graph SSU-from-tablehits.cwl

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 43d2fb8a5430dc56b55e84e3986d0079cad8d185
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 89ccbfc53ff3bb6abe2eb90bb7e0091c54c18f5c

Packed ID: main
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325
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: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 2decd55996b912feb48be5db1b052aa3274ee405
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: f1eb0f4eaaf1661044f28d859f7e8d4302525ead
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: f1eb0f4eaaf1661044f28d859f7e8d4302525ead