Explore Workflows

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: b0ee40d34d233f1611c2e2c66b6d22a3b7deec05

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: a409db2289b86779897ff19003bd351701a81c50

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: 60854b5d299df91e135e05d02f4be61f6a310fbc

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

Path: v1.0/v1.0/scatter-wf3.cwl

Branch/Commit ID: a5ae5ad0c9017ed625fb372f65e72dbb069439b0

Packed ID: main

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/harmonization_novoalign.cwl

Branch/Commit ID: 7f01768479e6a77a5caf6b3382174aa038ba05fc

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: gdc-dnaseq-aln-cwl/gdc_dnaseq.bamfastq_align.workflow.cwl

Branch/Commit ID: 03f751c7a4b37cd9dfaa70bef9ba3c4509e442cc

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: 77a9fa25b89ce73582a1ce6ba75fa6d2537fb8e8

What is MAnorm? -------------- MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets of TFs (transcription factors) or epigenetic modifications and you can use it for: * Normalization of two ChIP-seq samples * Quantitative comparison (differential analysis) of two ChIP-seq samples * Evaluating the overlap enrichment of the protein binding sites(peaks) * Elucidating underlying mechanisms of cell-type specific gene regulation How MAnorm works? ---------------- MAnorm uses common peaks of two samples as a reference to build the rescaling model for normalization, which is based on the empirical assumption that if a chromatin-associated protein has a substantial number of peaks shared in two conditions, the binding at these common regions will tend to be determined by similar mechanisms, and thus should exhibit similar global binding intensities across samples. The observed differences on common peaks are presumed to reflect the scaling relationship of ChIP-Seq signals between two samples, which can be applied to all peaks.

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

Path: workflows/manorm.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b

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

Path: tests/step-valuefrom5-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/qc-assembled.workflow.cwl

Branch/Commit ID: 81feefc84ec0faecf1ade718001d5f07610e616e