Explore Workflows

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_process.cwl

Branch/Commit ID: 302f1f3c019b74b85a4decc56c0793726e99c191

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: 12e5256de1b680c551c87fd5db6f3bc65428af67

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

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

Branch/Commit ID: 6e9f82a6d2195d4f16f28fd6e1485138372fb430

Packed ID: main

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

Path: definitions/pipelines/wgs.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc

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

Path: v1.0/v1.0/fail-unconnected.cwl

Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e

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

Path: tests/count-lines19-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/align_and_count.cwl

Branch/Commit ID: 11debf9ac656096a0c572c2d26b0980ee3ccb98b

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `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. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058

Single-cell RNA-Seq Aggregate Aggregates gene expression data from multiple Single-cell RNA-Seq Alignment experiments.

https://github.com/Barski-lab/sc-seq-analysis.git

Path: workflows/sc-rna-aggregate-wf.cwl

Branch/Commit ID: 9064af1cdd8e97bcdf4473e2a741e1ada1a7c4f3

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e