Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	bact_get_kmer_reference	https://github.com/ncbi/pgap.git Path: task_types/tt_bact_get_kmer_reference.cwl Branch/Commit ID: 16d1198871195e2229fd44dd0ad94a4ed6a87caf
	step-valuefrom-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944
	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: 3fc68366adb179927af5528c27b153abaf94494d
	tt_kmer_compare_wnode Pairwise comparison	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_compare_wnode.cwl Branch/Commit ID: a7fced3ed8c839272c8f3a8db9da7bc8cd50271f
	WGS QC workflow nonhuman	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_wgs_nonhuman.cwl Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
	mut3.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/mut3.cwl Branch/Commit ID: a94d75178c24ce77b59403fb8276af9ad1998929
	exome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome_mouse.cwl Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
	Xenbase RNA-Seq pipeline paired-end 1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump) 2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files) 3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ files to reference genome, calculate genes and isoforms expression (run RSEM) 5. Count mapped reads number in sorted BAM file (run bamtools stats) 6. Generate genome coverage BED file (run bedtools genomecov) 7. Sort genearted BED file (run sort) 8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)	https://github.com/datirium/workflows.git Path: workflows/xenbase-rnaseq-pe.cwl Branch/Commit ID: 2b8146f76595f0c4d8bf692de78b21280162b1d0
	Running cellranger count and lineage inference	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/single_cell_rnaseq.cwl Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
	wgs alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/tumor_only_wgs.cwl Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a