Explore Workflows

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

Graph	Name	Retrieved From	View
	BWA index pipeline This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.	https://github.com/datirium/workflows.git Path: workflows/bwa-index.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	taxonomy_check_16S	https://github.com/ncbi/pgap.git Path: task_types/tt_taxonomy_check_16S.cwl Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
	js-expr-req-wf.cwl#wf	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc Packed ID: wf
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
	Filter differentially expressed genes from DESeq for Tag Density Profile Analyses Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.	https://github.com/datirium/workflows.git Path: workflows/filter-deseq-for-heatmap.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	rnaseq-se-dutp.cwl Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.	https://github.com/Barski-lab/workflows.git Path: workflows/rnaseq-se-dutp.cwl Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d
	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: f906212e2c9a88280ae36545e5422f25752aa8f4
	Bismark Methylation SE Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).	https://github.com/datirium/workflows.git Path: workflows/bismark-methylation-se.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	Run pindel on provided region	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pindel_region.cwl Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2
	taxonomy_check_16S	https://github.com/ncbi/pgap.git Path: task_types/tt_taxonomy_check_16S.cwl Branch/Commit ID: 093b60e546237c06cfe7820d6ac8d66467e66725