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Graph	Name	Retrieved From	View
	Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.	https://github.com/datirium/workflows.git Path: workflows/filter-peaks-for-heatmap.cwl Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
	io-union-input-default-wf.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/io-union-input-default-wf.cwl Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df
	Trim Galore RNA-Seq pipeline paired-end The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) RNA-Seq basic analysis for a pair-end experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file	https://github.com/datirium/workflows.git Path: workflows/trim-rnaseq-pe.cwl Branch/Commit ID: 17a4a68b20e0af656e09714c1f39fe761b518686
	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: a7b031090f49ab52195a561c162b326998028a35
	no-inputs-wf.cwl Workflow without inputs.	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/no-inputs-wf.cwl Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
	Trim Galore RNA-Seq pipeline single-read strand specific Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) RNA-Seq basic analysis for a single-end experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file	https://github.com/datirium/workflows.git Path: workflows/trim-rnaseq-se-dutp.cwl Branch/Commit ID: 44214a9d02e6d85b03eb708552ed812ae3d4a733
	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: 9bf0aa495735f8081bb5870cb32fc898b9e6eb22
	allele-vcf-rnaseq-pe.cwl Allele specific RNA-Seq (using vcf) paired-end workflow	https://github.com/datirium/workflows.git Path: workflows/allele-vcf-rnaseq-pe.cwl Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf
	Cell Ranger Build Reference Indices Devel version of Cell Ranger Build Reference Indices pipeline =============================================================	https://github.com/datirium/workflows.git Path: workflows/cellranger-mkref.cwl Branch/Commit ID: e99e80a2c19682d59947bde04a892d7b6d90091c
	kmer_top_n_extract	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_top_n_extract.cwl Branch/Commit ID: 42712bca4c3307d87b6b55f525a4c97cb6f7e288