Explore Workflows

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5

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

Path: workflows/bamfastq_align/readgroup_fastq_pe.cwl

Branch/Commit ID: 0495e3095182b2e1b4d6274833b3d2ce30347a4e

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f

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

Path: definitions/pipelines/somatic_exome_nonhuman.cwl

Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 369afa7090a7480e6a0b144eff967a4a52b6fde2

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 SE sample 1** * previously analyzed ChIP-Seq single-read experiment to be used as Sample 1 **ChIP-Seq SE sample 2** * previously analyzed ChIP-Seq single-read 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-se.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 316831663e84623eb0e3a260af252fef441924d4