Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

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

Path: workflows/trim-rnaseq-pe.cwl

Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f

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

Path: v1.0/v1.0/count-lines13-wf.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_amplicon_kit.cwl

Branch/Commit ID: 6b43e8b03256492f2b36ffcf548704daaafee6f6

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: c235dc6d623879a6c4f5fb307f545c9806eb2d23

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 16d1198871195e2229fd44dd0ad94a4ed6a87caf

https://github.com/bcbio/bcbio_validation_workflows.git

Path: giab-joint/giab-joint-workflow/main-giab-joint.cwl

Branch/Commit ID: 24e9fff0d5e406323b826c0e8bd150be0ff8aba4

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 9c0b1497c467393e1a54735575043dced73e95c4

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f