Explore Workflows

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/YeoLab/eclip.git

Path: cwl/wf_trim_and_map_se_nostats.cwl

Branch/Commit ID: b389f7fe3e76cb6e3f31c3a8e2e3b59bb400e74c

https://github.com/ncbi/pgap.git

Path: vecscreen/vecscreen.cwl

Branch/Commit ID: 94c97cfc95a5bf102a6f9206e045ea1afb768317

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/haplotypecaller.cwl

Branch/Commit ID: 7f01768479e6a77a5caf6b3382174aa038ba05fc

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/download_check.cwl

Branch/Commit ID: 7f01768479e6a77a5caf6b3382174aa038ba05fc

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/dev/ultra-opt/workflows/kfdrc_bwamem_subwf.cwl

Branch/Commit ID: fc947e792856747f8dbd78811ee105dbd736bea6

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/joint_genotype.cwl

Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022

CNV GRIDSS calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/cnv_gridss.cwl

Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_dispatch/workflow.cwl

Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729

https://github.com/ncbi/pgap.git

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: d218e081d8f6a4fdab56a38ce0fc2fae6216cecc

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_dispatch/2blat/workflow.cwl

Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729