Explore Workflows

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

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe

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 **single-read** experiment with Trim Galore. The pipeline was adapted for ATAC-Seq single-read data analysis by updating genome coverage step. _Trim Galore_ is a wrapper around [Cutadapt](https://github.com/marcelm/cutadapt) and [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. In outputs it returns coordinate sorted BAM file alongside with index BAI file, quality statistics of the input FASTQ file, reads coverage in a form of 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 (on the base of BAM file). 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 unsorted SAM file which is being sorted and indexed by `samtools sort` and `samtools index` *samtools\_sort\_index*. Based 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 input BAM and BAI files return. Otherwise step *samtools\_sort\_index\_after\_rmdup* repeat `samtools sort` and `samtools index` with BAM and BAI files. Right after that `macs2 callpeak` performs peak calling *macs2\_callpeak*. On the base of returned outputs the next step *macs2\_island\_count* calculates the number of islands and estimated fragment size. If the last one is less that 80bp (hardcoded in the workflow) `macs2 callpeak` is rerun again with forced fixed fragment size value (*macs2\_callpeak\_forced*). If at the very beginning it was set in workflow input parameters to force run peak calling with fixed fragment size, this step is skipped and the original peak calling results are saved. In the next step workflow again calculates the number of islands and estimates fragment size (*macs2\_island\_count\_forced*) for the data obtained from *macs2\_callpeak\_forced* step. If the last one was skipped the results from *macs2\_island\_count\_forced* step are equal to the ones obtained from *macs2\_island\_count* step. 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 on the base of input BAM file and save it in BigWig format. For that purpose bamtools stats returns the number of mapped reads number which is then used as scaling factor by bedtools genomecov when it performs coverage calculation and saves it in BED format. The last one is then being sorted and converted to BigWig format by bedGraphToBigWig tool from UCSC utilities. To adapt the pipeline for ATAC-Seq data analysis we calculate genome coverage using only the first 9 bp from every read. 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 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 on the base of BAM file.

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

Path: workflows/trim-atacseq-se.cwl

Branch/Commit ID: a68821bf3a9ceadc3b2ffbb535d601d9a645b377

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: c5bae2ca862c764911b83d1f15ff6af4e2a0db28

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

Path: testdata/step-valuefrom3-wf_v1_1.cwl

Branch/Commit ID: c1875d54dedc41b1d2fa08634dcf1caa8f1bc631

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

Path: definitions/pipelines/umi_molecular_alignment.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f

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

Path: tests/count-lines7-wf.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: be465ad19b07378f3f863f2c4e0019b420c859f2

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: f18c1dce463509170ee3bf2844d5a3637ff706f5

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 55b6ee46b0c9fb1c9949cd0888b388c6f11b73b1

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c