Explore Workflows

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3

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: 17a4a68b20e0af656e09714c1f39fe761b518686

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0

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

Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc

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

Path: definitions/pipelines/germline_exome_gvcf.cwl

Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca

Packed ID: main

GSEAPY: Gene Set Enrichment Analysis in Python ============================================== Gene Set Enrichment Analysis is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA requires as input an expression dataset, which contains expression profiles for multiple samples. While the software supports multiple input file formats for these datasets, the tab-delimited GCT format is the most common. The first column of the GCT file contains feature identifiers (gene ids or symbols in the case of data derived from RNA-Seq experiments). The second column contains a description of the feature; this column is ignored by GSEA and may be filled with “NA”s. Subsequent columns contain the expression values for each feature, with one sample's expression value per column. It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived. The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. Tools such as DESeq2 can be made to produce properly normalized data (normalized counts) which are compatible with GSEA. Documents ============================================== - GSEA Home Page: https://www.gsea-msigdb.org/gsea/index.jsp - Results Interpretation: https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Interpreting_GSEA_Results - GSEA User Guide: https://gseapy.readthedocs.io/en/latest/faq.html - GSEAPY Docs: https://gseapy.readthedocs.io/en/latest/introduction.html References ============================================== - Subramanian, Tamayo, et al. (2005, PNAS), https://www.pnas.org/content/102/43/15545 - Mootha, Lindgren, et al. (2003, Nature Genetics), http://www.nature.com/ng/journal/v34/n3/abs/ng1180.html

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

Path: workflows/gseapy.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f

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

Path: cwltool/schemas/v1.0/v1.0/sum-wf.cwl

Branch/Commit ID: 047e69bb169e79fad6a7285ee798c4ecec3b218b

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_bcftools_annotate_module.cwl

Branch/Commit ID: 462aaebbd442e84ea101b45b716df0174b88512e