Explore Workflows

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

Path: testdata/workflow_input_sf_expr.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0

For a given Zenodo community, retrieve its repository records as Zenodo JSON and (eventually) schema.org JSON-LD and DataCite v4 XML.

https://github.com/stain/ro-index-paper.git

Path: code/data-gathering/workflows/zenodo-records.cwl

Branch/Commit ID: b43b2bf099406a606f1a873baa3452ec8888c7dd

Single-cell ATAC-Seq Differential Binding Analysis Identifies differential bound sites between two groups of cells

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

Path: workflows/sc-atac-dbinding.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: cabb1a9a95244e93294727be8cf5816c38992cb0

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

https://github.com/Barski-lab/workflows.git

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 80d64741638b14de5cf58236b6d6d99713c62086

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 252e7214ac64cb1128881e76743013e61bc7ec38

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944

https://github.com/wtsi-hgi/arvados-pipelines.git

Path: cwl/workflows/gatk-4.0.0.0-genomics-db-and-genotypegvcfs-per-interval-list.cwl

Branch/Commit ID: 95babe5d8779c036e3499940544c7709600929d1

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **ChIP-Seq** basic analysis workflow for a **paired-end** experiment. A [FASTQ](http://maq.sourceforge.net/fastq.shtml) input file has to be provided. The pipeline produces a sorted BAM file alongside with index BAI file, quality statistics of the input FASTQ file, coverage by estimated fragments as a BigWig file, peaks calling data in a form of narrowPeak or broadPeak files, islands with the assigned nearest genes and region type, data for average tag density plot. Workflow starts with step *fastx\_quality\_stats* from FASTX-Toolkit to calculate quality statistics for input FASTQ file. At the same time `bowtie` is used to align reads from input FASTQ file to reference genome *bowtie\_aligner*. The output of this step is an unsorted SAM file which is being sorted and indexed by `samtools sort` and `samtools index` *samtools\_sort\_index*. Depending on workflow’s input parameters indexed and sorted BAM file can be processed by `samtools rmdup` *samtools\_rmdup* to get rid of duplicated reads. If removing duplicates is not required the original BAM and BAI files are returned. Otherwise step *samtools\_sort\_index\_after\_rmdup* repeat `samtools sort` and `samtools index` with BAM and BAI files without duplicates. Next `macs2 callpeak` performs peak calling *macs2\_callpeak* and the next step reports *macs2\_island\_count* the number of islands and estimated fragment size. If the latter is less that 80bp (hardcoded in the workflow) `macs2 callpeak` is rerun again with forced fixed fragment size value (*macs2\_callpeak\_forced*). It is also possible to force MACS2 to use pre set fragment size in the first place. Next step (*macs2\_stat*) is used to define which of the islands and estimated fragment size should be used in workflow output: either from *macs2\_island\_count* step or from *macs2\_island\_count\_forced* step. If input trigger of this step is set to True it means that *macs2\_callpeak\_forced* step was run and it returned different from *macs2\_callpeak* step results, so *macs2\_stat* step should return [fragments\_new, fragments\_old, islands\_new], if trigger is False the step returns [fragments\_old, fragments\_old, islands\_old], where sufix \"old\" defines results obtained from *macs2\_island\_count* step and sufix \"new\" - from *macs2\_island\_count\_forced* step. The following two steps (*bamtools\_stats* and *bam\_to\_bigwig*) are used to calculate coverage from BAM file and save it in BigWig format. For that purpose bamtools stats returns the number of mapped reads which is then used as scaling factor by bedtools genomecov when it performs coverage calculation and saves it as a BEDgraph file whichis then sorted and converted to BigWig format by bedGraphToBigWig tool from UCSC utilities. Step *get\_stat* is used to return a text file with statistics in a form of [TOTAL, ALIGNED, SUPRESSED, USED] reads count. Step *island\_intersect* assigns nearest genes and regions to the islands obtained from *macs2\_callpeak\_forced*. Step *average\_tag\_density* is used to calculate data for average tag density plot from the BAM file.

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

Path: workflows/chipseq-pe.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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

Path: workflows/fastqc.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa