Explore Workflows

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: e668f9c4047f1971ae53040a5af3eccc4bfc3c53

https://github.com/adamscharlotte/CWL-workflow.git

Path: Protein_Inference_workflow.cwl

Branch/Commit ID: 90e89d0feac36a1cadbac0625a32ff6b1ee715fb

curl will download a HTTP/HTTPS resource or file from a given URL, following any redirections.

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

Path: code/data-gathering/workflows/zip-content-by-url.cwl

Branch/Commit ID: eba15168698e62150c10924bd7b2fa1ff1f0c85a

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: f390475a4e0898d4933f0a28dae278aa35803eb1

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: 87f213456b3f966b773d396cce1fe5a272dad858

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: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

Single-Cell RNA-Seq Cluster Analysis Clusters cells by similarity of gene expression data from the outputs of the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” pipeline. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, and “Single-Cell Differential Abundance Analysis” pipelines.

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

Path: workflows/sc-rna-cluster.cwl

Branch/Commit ID: 549fac35bf6b8b1c25af0f4f6c3f162c40dc130e

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

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

Path: tests/wf/revsort_step_bad_schema.cwl

Branch/Commit ID: 6cfef62c21330672538fd5e9b45ec888569c0a6f

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines11-wf-noET.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 7f9cfcbda5998b164bd1d8f1f6006aefda0f47f3