Explore Workflows

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Graph Name Retrieved From View
workflow graph ST520112.cwl

https://github.com/Marco-Salvi/dtc51.git

Path: ST520112.cwl

Branch/Commit ID: 272db37d2b8108a146769f0fb0383bb824c9788f
workflow graph ST520110.cwl

https://github.com/Marco-Salvi/dtc51.git

Path: ST520110.cwl

Branch/Commit ID: 272db37d2b8108a146769f0fb0383bb824c9788f
workflow graph Single-Cell ATAC-Seq Genome Coverage

Single-Cell ATAC-Seq Genome Coverage Generates genome coverage tracks from chromatin accessibility data of selected cells

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

Path: workflows/sc-atac-coverage.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: f403d9e26d60d3e3591a03077bc9dfa188b1c2bb
workflow graph Chipseq alignment for nonhuman with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq_alignment_nonhuman.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2
workflow graph 1st-workflow.cwl

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: d64178072bc4fc9700ab80cdf90146890b96587e
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
workflow graph Bismark Methylation SE

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: 36fd18f11e939d3908b1eca8d2939402f7a99b0f