Explore Workflows

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

Graph	Name	Retrieved From	View
	BioExcel-CWL-MDSetup.cwl	https://github.com/bioexcel/biobb_wf_cwl_tutorial.git Path: biobb_wf_cwl_tutorial/examples/BioExcel-CWL-MDSetup.cwl Branch/Commit ID: 0d77918a9347b12af11fe71273b0c1f9dccbd2d3
	varscanW.cwl Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using VARSCAN. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.	https://github.com/ambarishK/bio-cwl-tools.git Path: varscanW.cwl Branch/Commit ID: 690ff2fa1ef356c42003e4b9986d39f4e44806a8
	assm_assm_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 0514ffe248dd11068a3f2268bc67b6ce5ab051d2
	Apply filters to VCF file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: 3bb0693076adc1543079a6b136c74906ad546ac6
	BioExcel-CWL-MDSetup.cwl	https://github.com/longr/biobb_wf_cwl_tutorial.git Path: biobb_wf_cwl_tutorial/examples/BioExcel-CWL-MDSetup.cwl Branch/Commit ID: 0d77918a9347b12af11fe71273b0c1f9dccbd2d3
	Create Genomic Collection for Bacterial Pipeline, ASN.1 input	https://github.com/ncbi/pgap.git Path: genomic_source/wf_genomic_source_asn.cwl Branch/Commit ID: f225cd99b0e0a5043dd102f8b33a6139fefe9ea4
	Bismark Methylation - pipeline for BS-Seq data analysis 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: b957a4f681bf0ca8ebba4e0d0ec3936bf79620c5
	Transcriptome Vector Detection This workflow detect and remove vector from a transcriptome fasta file	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/Annotation/transcriptome-vector-detection.cwl Branch/Commit ID: 2667814192299c0c7b4d23c6edb697b6cd636286
	wffail.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/wffail.cwl Branch/Commit ID: e6c2d955a448225f026a04130443d13661844440
	cluster_blastp_wnode and gpx_qdump combined	https://github.com/ncbi/pgap.git Path: task_types/tt_cluster_and_qdump.cwl Branch/Commit ID: 2229f26ec424f9ebeb3db7fec3bd3f84a38c7485