Explore Workflows

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

Path: workflows/bamfastq_align/extract_readgroups_bam_http.cwl

Branch/Commit ID: 8edf6a5e4e7790434ad0742e50d0c97a5d0bb846

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines9-wf.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37

BAM filtering

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

Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl

Branch/Commit ID: b62c7bfcf5eb7ac3c1ed06879200fdf5db947e4b

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: 4360fb2e778ecee42e5f78f83b78c65ab3a2b1df

Cellranger Reanalyze ====================

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620

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. What do the inputs mean? ---------------- ### General **Experiment short name/Alias** * short name for you experiment to identify among the others **ChIP-Seq PE sample 1** * previously analyzed ChIP-Seq paired-end experiment to be used as Sample 1 **ChIP-Seq PE sample 2** * previously analyzed ChIP-Seq paired-end experiment to be used as Sample 2 **Genome** * Reference genome to be used for gene assigning ### Advanced **Reads shift size for sample 1** * This value is used to shift reads towards 3' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **Reads shift size for sample 2** * This value is used to shift reads towards 5' direction to determine the precise binding site. Set as half of the fragment length. Default 100 **M-value (log2-ratio) cutoff** * Absolute M-value (log2-ratio) cutoff to define biased (differential binding) peaks. Default: 1.0 **P-value cutoff** * P-value cutoff to define biased peaks. Default: 0.01 **Window size** * Window size to count reads and calculate read densities. 2000 is recommended for sharp histone marks like H3K4me3 and H3K27ac, and 1000 for TFs or DNase-seq. Default: 2000

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

Path: workflows/manorm-pe.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 03af16c9df2ee77485d4ab092cd64ae096d2e71c

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 7518b100d8cbc80c8be32e9e939dfbb27d6b4361

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

Path: workflows/bamfastq_align/extract_readgroup_fastq_se_http.cwl

Branch/Commit ID: 8edf6a5e4e7790434ad0742e50d0c97a5d0bb846

CNV ExomeDepth calling

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

Path: structuralvariants/cwl/subworkflows/cnv_exome_depth.cwl

Branch/Commit ID: b62c7bfcf5eb7ac3c1ed06879200fdf5db947e4b