Explore Workflows

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

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: ef7f3345b352319ec22dffba26c79df033b141f9

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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

Path: workflows/fastqc.cwl

Branch/Commit ID: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86

BAM filtering

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

Path: structuralvariants/subworkflows/bam_filtering.cwl

Branch/Commit ID: c494fa4f60d9215842c4d2c75ed7d89757435b0f

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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/rnaseq-pe-dutp.cwl

Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/ABRA/abra_workflow.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3

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

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

Branch/Commit ID: 7bfd77118cdc80dd7150115dd7a1a7ee6046f6fe

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e

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

Path: metadata/chipseq-header.cwl

Branch/Commit ID: 1f03ff02ef829bdb9d582825bcd4ca239e84ca2e

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

Path: tests/count-lines11-wf-noET.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b

Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals.

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

Path: workflows/bedtools-multicov.cwl

Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c