Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63

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

Path: tests/io-int-wf.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b

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

Path: tests/scatter-valuefrom-wf4.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b

Packed ID: main

Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).

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

Path: workflows/bismark-methylation-se.cwl

Branch/Commit ID: 1a46cb0e8f973481fe5ae3ae6188a41622c8532e

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/ABRA/abra_workflow.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f

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: 8a92669a566589d80fde9d151054ffc220ed4ddd

Workflow for Metagenomics binning from assembly.<br> Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file Summary - MetaBAT2 (binning) - MaxBin2 (binning) - SemiBin (binning) - DAS Tool (bin merging) - EukRep (eukaryotic classification) - CheckM (bin completeness and contamination) - BUSCO (bin completeness) - GTDB-Tk (bin taxonomic classification) Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default<br><br> **All tool CWL files and other workflows can be found here:**<br> Tools: https://gitlab.com/m-unlock/cwl<br> Workflows: https://gitlab.com/m-unlock/cwl/workflows<br> **How to setup and use an UNLOCK workflow:**<br> https://m-unlock.gitlab.io/docs/setup/setup.html<br>

https://gitlab.com/m-unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_binning.cwl

Branch/Commit ID: 50aaa5a89d0cd01c80d55fb68dd72708d3796503

https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git

Path: Assembly/workflow/assembly-wf-virus.cwl

Branch/Commit ID: 9cb4f73c8b490faebcc39fdd6fe37f693a2e5213

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7