Explore Workflows

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: c6bfa0de917efb536dd385624fc7702e6748e61d

Workflow makes indices for [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886). It performs the following steps: 1. Runs `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Transforms array of files into [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file as an output

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

Path: workflows/star-index.cwl

Branch/Commit ID: 9ee330737f4603e4e959ffe786fbb2046db70a00

Single-cell Label Integration Analysis Harmonizes conflicting annotations in single-cell genomics studies.

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

Path: workflows/sc-triangulate.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e

Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed)

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/trimmed_fastq.cwl

Branch/Commit ID: 6ccec9c5c5bc9fb4e75ca0b9cc22d13df9ffb815

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 205f4ceb47ba7537a6923d2dfb03668317c2fd89

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

Path: cwltool/schemas/v1.0/v1.0/dynresreq-workflow.cwl

Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: a7fced3ed8c839272c8f3a8db9da7bc8cd50271f

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

Path: testdata/record-output-wf_v1_1.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

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

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d