Explore Workflows

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 807fe40bca1fbd18ede6250851b9f71de98da69b

https://github.com/nal-i5k/organism_onboarding.git

Path: MoveData-workflow.cwl

Branch/Commit ID: add45db6f08de518e224bdc3c04094fd69cad2d2

Cell Ranger Build Reference Indices ===================================

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

Path: workflows/cellranger-mkref.cwl

Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: 6a55118f915e24d2ad008c93a02d9de5643f5511

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: 87f213456b3f966b773d396cce1fe5a272dad858

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-pe.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 99066c338467af54064cc4eb1be7ea863a785202

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: b5e16e359007150647b14dc6e038f4eb8dccda79

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: 4dcc405133f22c63478b6091fb5f591b6be8950f

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

Path: definitions/pipelines/somatic_exome_mouse.cwl

Branch/Commit ID: 789267ce0e3fed674ea5212a562315218fcf1bfc