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Graph Name Retrieved From View
workflow graph 03-map-se-blacklist-removal.cwl

ATAC-seq 03 mapping - reads: SE - blacklist removal

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
workflow graph mergeAndMarkBams_4_1_3.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/mergeAndMarkBams_4_1_3.cwl

Branch/Commit ID: 5ba65e4781f03a74a845b7cd40bbf4c2ae3a9844
workflow graph Get Proteins

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

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_nonhuman.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
workflow graph count-lines13-wf.cwl

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

Path: v1.0/v1.0/count-lines13-wf.cwl

Branch/Commit ID: 4fe434e969c93c94b690ba72db295d9d52a6f576
workflow graph pipeline-pe.cwl

ATAC-seq pipeline - reads: PE

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

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

Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1
workflow graph 03-map-pe-blacklist-removal.cwl

ATAC-seq 03 mapping - reads: PE - blacklist removal

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

Path: v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl

Branch/Commit ID: 67e8ccd5abddbd9e27f23ceeb95536fecf792d93
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: 104059e07a2964673e21d371763e33c0afeb2d03