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Graph	Name	Retrieved From	View
	format_rrnas_from_seq_entry	https://github.com/ncbi/pgap.git Path: task_types/tt_format_rrnas_from_seq_entry.cwl Branch/Commit ID: 61e3752f1f5e2ee498fa024c235226f8580be942
	ChIP-Seq pipeline paired-end 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: 46a077b51619c6a14f85e0aa5260ae8a04426fab
	cluster_blastp_wnode and gpx_qdump combined	https://github.com/ncbi/pgap.git Path: task_types/tt_cluster_and_qdump.cwl Branch/Commit ID: 664e99a23a3ed4ba36c08323ac597c4fbcd88df1
	tt_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: 664e99a23a3ed4ba36c08323ac597c4fbcd88df1
	EMG pipeline v3.0 (paired end version)	https://github.com/proteinswebteam/ebi-metagenomics-cwl.git Path: workflows/emg-pipeline-v3-paired.cwl Branch/Commit ID: cac44f2cf14110fde9951161c663c4525772f616
	cnv_exomedepth CNV ExomeDepth calling	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c
	align_merge_sas	https://github.com/ncbi/pgap.git Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: c18a7e5164cb6b19f06b3d1e869407c118a87f7e
	allele-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/Barski-lab/workflows.git Path: subworkflows/allele-alignreads-se-pe.cwl Branch/Commit ID: 378f693ebfb3edf9f589007e366fec1195ec1464
	super-enhancer.cwl Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl)	https://github.com/Barski-lab/workflows.git Path: workflows/super-enhancer.cwl Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7
	cnv_manta CNV Manta calling	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_manta.cwl Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c