Explore Workflows

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Graph	Name	Retrieved From	View
	gp_makeblastdb	https://github.com/ncbi/pgap.git Path: progs/gp_makeblastdb.cwl Branch/Commit ID: 7f857f7f2d7c080d27c775b67a6d6f7d94bce31f
	count-lines1-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/count-lines1-wf.cwl Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb
	SoupX Estimate SoupX Estimate ==============	https://github.com/datirium/workflows.git Path: workflows/soupx.cwl Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca
	Gene expression merge - combines RPKM gene expression from several experiments Gene expression merge - combines RPKM gene expression from several experiments =================================================================================== Workflows merges RPKM gene expression from several experiments based on the values from GeneId, Chrom, TxStart, TxEnd and Strand columns. Reported RPKM columns are renamed based on the experiments names.	https://github.com/datirium/workflows.git Path: workflows/feature-merge.cwl Branch/Commit ID: 2c486543c335bb99b245dfe7e2f033f535efb9cf
	screen out taxa Remove sequences which align against a reference set using bowtie2. The references are preformatted (index files)	https://github.com/MG-RAST/pipeline.git Path: CWL/Workflows/organism-screening.workflow.cwl Branch/Commit ID: 662d424d2e433e636f46a79025325d5daaca6271
	rna amplicon analysis for fastq files RNAs - qc, preprocess, annotation, index, abundance	https://github.com/MG-RAST/pipeline.git Path: CWL/Workflows/amplicon-fastq.workflow.cwl Branch/Commit ID: f5839797da8209a9d3e441023f88130219751020
	Build Bismark indices Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.	https://github.com/datirium/workflows.git Path: workflows/bismark-index.cwl Branch/Commit ID: 12c29f88855329192bfff977f046990031f04931
	preprocess fasta Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.	https://github.com/MG-RAST/pipeline.git Path: CWL/Workflows/preprocess-fasta.workflow.cwl Branch/Commit ID: 662d424d2e433e636f46a79025325d5daaca6271
	Run pindel on provided region	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pindel_region.cwl Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0
	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: e0a30aa1ad516dd2ec0e9ce006428964b840daf4