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Graph	Name	Retrieved From	View
	Cell Ranger Reference (RNA, ATAC, RNA+ATAC) Cell Ranger Reference (RNA, ATAC, RNA+ATAC) Builds a reference genome of a selected species for quantifying gene expression and chromatin accessibility. The results of this workflow are used in all “Cell Ranger Count” and “Cell Ranger Aggregate” pipelines.	https://github.com/datirium/workflows.git Path: workflows/cellranger-mkref.cwl Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
	Non-Coding Bacterial Genes	https://github.com/ncbi/pgap.git Path: bacterial_noncoding/wf_bacterial_noncoding.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
	rRNA_selection.cwl	https://github.com/proteinswebteam/ebi-metagenomics-cwl.git Path: tools/rRNA_selection.cwl Branch/Commit ID: 5e8217435bcdd597b2ad236f3e847d13d4c21824
	spurious_annot	https://github.com/ncbi/pgap.git Path: spurious_annot/wf_spurious_annot_pass1.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
	Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)	https://github.com/ncbi/pgap.git Path: bacterial_annot/wf_bacterial_annot_pass2.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
	Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)	https://github.com/ncbi/pgap.git Path: bacterial_annot/wf_bacterial_annot_pass3.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
	tRNA_selection.cwl	https://github.com/proteinswebteam/ebi-metagenomics-cwl.git Path: tools/tRNA_selection.cwl Branch/Commit ID: 5e8217435bcdd597b2ad236f3e847d13d4c21824
	Run tRNAScan	https://github.com/ncbi/pgap.git Path: bacterial_trna/wf_trnascan.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
	mergeAndMarkBams_4_1_3.cwl	https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git Path: janis_pipelines/wgs_somatic/cwl/tools/mergeAndMarkBams_4_1_3.cwl Branch/Commit ID: d919f2dd335da64a4fa352df9ea1b27ba13edad8
	Get Proteins	https://github.com/ncbi/pgap.git Path: wf_bacterial_prot_src.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf