Explore Workflows

Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.

https://github.com/MG-RAST/qiime-pipeline.git

Path: CWL/Workflows/qiime/demultiplexed-fasta2taxa-summary-plot.cwl

Branch/Commit ID: 4304c60b6e2e7980ad1d659f4b904730ce9c0706

https://github.com/EBI-Metagenomics/CWL-assembly.git

Path: tools/stats/coverage.cwl

Branch/Commit ID: 6d5695af158f4513ce383bb2b15319449f7ddb07

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/readgroup_fastq_se.cwl

Branch/Commit ID: cf2e9d7c3cc87ce97a1fbf73fad574b170fedcfb

https://github.com/FarahZKhan/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: bcfe5f9affd23d52467f69b4b21d1098f0ca95d7

https://github.com/idaks/cwl_modeling.git

Path: yw_cwl_modeling/yw_cwl_parser_old/Examples/exec_paleocar/wf_exec_paleocar.cwl

Branch/Commit ID: cd1454539fc62c7a9a66de56459610728dec8baa

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/readgroup_fastq_pe.cwl

Branch/Commit ID: cf2e9d7c3cc87ce97a1fbf73fad574b170fedcfb

This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs

https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git

Path: qa_check_subwf.cwl

Branch/Commit ID: 6366ed398da10019b6d81a789291af6d909f28f4

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

Path: workflows/kfdrc_cram_to_gvcf.cwl

Branch/Commit ID: b8b1a96d015db74ea451bb7bf83a5e48e645ce1f

https://github.com/EBI-Metagenomics/CWL-assembly.git

Path: tools/metaspades_pipeline.cwl

Branch/Commit ID: 6d5695af158f4513ce383bb2b15319449f7ddb07

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/integrity.cwl

Branch/Commit ID: cf2e9d7c3cc87ce97a1fbf73fad574b170fedcfb