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: d76110e0bfc40c874f82e37cef6451d74df4f908

https://github.com/BerndDoser/Spherinator.git

Path: streamflow/hipster.cwl

Branch/Commit ID: 34cce5b7986a0b130b661804a7bc67176b1fb6ad

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-002.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

https://github.com/BAMresearch/NFDI4IngScientificWorkflowRequirements.git

Path: exemplary_workflow/cwl/wf_run_exemplary_wf.cwl

Branch/Commit ID: 57de8f8d91892a17578d69249cb790e3022be042

Plot and compare array element coordinates. Validate coordinate transformation from those used in observatory database to simulation systems.

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

Path: workflows/ValidateArrayElementCoordinates.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c

https://github.com/NCI-GDC/gdc-rnaseq-cwl.git

Path: rnaseq-star-align/subworkflows/rnaseq_processing/star_align_workflow.cwl

Branch/Commit ID: 88fb720c62a3c2b00ca475d412fba088c4a08f92

Calculate effective focal length for the given telescope optics.

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

Path: workflows/SetEffectiveFocalLength.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7

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

Path: v1.0/v1.0/scatter-wf3.cwl

Branch/Commit ID: 9a23706ec061c5d2c02ff60238d218aadf0b5db9

Packed ID: main