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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: 261c0232a7a40880f2480b811ed2d7e89c463869

https://github.com/mskcc/argos-cwl.git

Path: modules/pair/realignment.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6

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

Path: v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl

Branch/Commit ID: 5c7799a145595323d0a8628be1fe0e24985e793a

Packed ID: main

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/Barski-lab/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 7826a52718f052b53cc3872dcb3619a61babb44b

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_sentieon_gvcf_wf.cwl

Branch/Commit ID: 4b8dc1e00d3dd082ee31629afdeda6103f75dc3a

https://github.com/kids-first/kf-rnaseq-workflow.git

Path: workflow/kfdrc_annoFuse_wf.cwl

Branch/Commit ID: 65161d6565c436a7b1e0b3be56efb433a994ed9d

Cell Ranger Aggregate =====================

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

Path: workflows/cellranger-aggr.cwl

Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d

Single-cell Manual Cell Type Assignment Assigns cell types for clusters based on the provided metadata file.

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

Path: workflows/sc-ctype-assign.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe