Explore Workflows

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

Path: testdata/step_valuefrom5_wf_v1_1.cwl

Branch/Commit ID: c46a3ad4e488e75b7a58032c129f0605f5e84f40

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: e238d1756f1db35571e84d72e1699e5d1540f10c

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: gatk4-mutect2-tumor-only-cwl/gpas_gatk4.2.4.1_mutect2_tumor_only_workflow.cwl

Branch/Commit ID: 4a93f8fcd34a25427b4ade8afe1772a3287fcf1e

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

Path: tests/wf/iwdr-passthrough-successive.cwl

Branch/Commit ID: 67df61c8b3ea11f00d5f24c016e540b5c146d759

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

Path: tests/step-valuefrom5-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

Allele specific RNA-Seq (using vcf) single-read workflow

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

Path: workflows/allele-vcf-rnaseq-se.cwl

Branch/Commit ID: e238d1756f1db35571e84d72e1699e5d1540f10c

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

Path: definitions/pipelines/germline_exome_gvcf.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c

https://github.com/mskcc/argos-cwl.git

Path: modules/pair/collect_pair_files.cwl

Branch/Commit ID: 7c694b51d9d593439cf8ab3e5006665f0bbe2149

https://github.com/sentieon/sentieon-cwl.git

Path: stage/bwa-mem-sort-distr.cwl

Branch/Commit ID: d20382adfe7285cb517a25d95d2bcb7586546e23

https://github.com/UoMResearchIT/wrf_emep_cwl_linear_workflow.git

Path: workflows/geogrid_workflow.cwl

Branch/Commit ID: 70c6a6016eeb4434a3ad82af7908b83d4ea37ce7