Explore Workflows

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Graph Name Retrieved From View
workflow graph readgroup_fastq_se.cwl

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

Path: workflows/bamfastq_align/readgroup_fastq_se.cwl

Branch/Commit ID: 0495e3095182b2e1b4d6274833b3d2ce30347a4e
workflow graph SoupX Estimate

SoupX Estimate ==============

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

Path: workflows/soupx.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph MAnorm PE - quantitative comparison of ChIP-Seq paired-end data

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: 581156366f91861bd4dbb5bcb59f67d468b32af3
workflow graph epigenome-chip-seq.packed.cwl#macs2.cwl

https://github.com/pitagora-network/DAT2-cwl.git

Path: workflow/epigenome-chip-seq/epigenome-chip-seq.packed.cwl

Branch/Commit ID: 0cd20e1be620ae0817a1aa4286d73b78c89809f0

Packed ID: macs2.cwl
workflow graph Metagenomics workflow

Workflow pilon assembly polishing Steps: - BBmap (Read mapping to assembly) - Pilon

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_pilon_mapping.cwl

Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 18600518ce6539a2e29c1707392a4c5da5687fa3
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 90a321ecf2d049330bcf0657cc4d764d2c3f42dd
workflow graph Filter differentially expressed genes from DESeq for Tag Density Profile Analyses

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

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

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: 60854b5d299df91e135e05d02f4be61f6a310fbc
workflow graph trick_revsort.cwl

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

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

Path: tests/wf/trick_revsort.cwl

Branch/Commit ID: aec33fcfa3459a90cbba8c88ebb991be94d21429