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Graph	Name	Retrieved From	View
	waltz_workflow_all_bams.cwl	https://github.com/mskcc/ACCESS-Pipeline.git Path: workflows/waltz/waltz_workflow_all_bams.cwl Branch/Commit ID: 09ddd9711fb550f56d52f1806cdefd4a8cd943b0
	Trim Galore ATAC-Seq pipeline single-read 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: ad948b2691ef7f0f34de38f0102c3cd6f5182b29
	wgs alignment with qc	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_wgs.cwl Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
	Exome QC workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
	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: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
	Unaligned bam to sorted, markduped bam	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/align_sort_markdup.cwl Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
	exome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome.cwl Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
	allele-vcf-alignreads-se-pe.cwl Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.	https://github.com/datirium/workflows.git Path: subworkflows/allele-vcf-alignreads-se-pe.cwl Branch/Commit ID: 6e09b4bf1ff0eb3dd1294f5578624c5a2a2b0b37
	wf-loadContents.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/wf-loadContents.cwl Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df
	standard_pipeline.cwl This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2	https://github.com/mskcc/ACCESS-Pipeline.git Path: workflows/standard_pipeline.cwl Branch/Commit ID: 0bd60a8962cc9960b7e4f6528547e220bcd2b941