Explore Workflows

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

Graph Name Retrieved From View
workflow graph wf-alignment.cwl

https://github.com/garyluu/bcbio_validation_workflows.git

Path: wes-agha-test/wes_chr21_test-workflow-gcp/wf-alignment.cwl

Branch/Commit ID: master
workflow graph RNASelector as a CWL workflow

https://doi.org/10.1007/s12275-011-1213-z

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

Path: workflows/rna-selector.cwl

Branch/Commit ID: 3039744
workflow graph pipeline-pe-blacklist-removal.cwl

ATAC-seq pipeline - reads: PE - with blacklist removal

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl

Branch/Commit ID: master
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: low-vaf
workflow graph EMG pipeline's QIIME workflow

Step 1: Set environment PYTHONPATH, QIIME_ROOT, PATH Step 2: Run QIIME script pick_closed_reference_otus.py ${python} ${qiimeDir}/bin/pick_closed_reference_otus.py -i $1 -o $2 -r ${qiimeDir}/gg_13_8_otus/rep_set/97_otus.fasta -t ${qiimeDir}/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt -p ${qiimeDir}/cr_otus_parameters.txt Step 3: Convert new biom format to old biom format (json) ${qiimeDir}/bin/biom convert -i ${resultDir}/cr_otus/otu_table.biom -o ${resultDir}/cr_otus/${infileBase}_otu_table_json.biom --table-type=\"OTU table\" --to-json Step 4: Convert new biom format to a classic OTU table. ${qiimeDir}/bin/biom convert -i ${resultDir}/cr_otus/otu_table.biom -o ${resultDir}/cr_otus/${infileBase}_otu_table.txt --to-tsv --header-key taxonomy --table-type \"OTU table\" Step 5: Create otu summary ${qiimeDir}/bin/biom summarize-table -i ${resultDir}/cr_otus/otu_table.biom -o ${resultDir}/cr_otus/${infileBase}_otu_table_summary.txt Step 6: Move one of the result files mv ${resultDir}/cr_otus/otu_table.biom ${resultDir}/cr_otus/${infileBase}_otu_table_hdf5.biom Step 7: Create a list of observations awk '{print $1}' ${resultDir}/cr_otus/${infileBase}_otu_table.txt | sed '/#/d' > ${resultDir}/cr_otus/${infileBase}_otu_observations.txt Step 8: Create a phylogenetic tree by pruning GreenGenes and keeping observed otus ${python} ${qiimeDir}/bin/filter_tree.py -i ${qiimeDir}/gg_13_8_otus/trees/97_otus.tree -t ${resultDir}/cr_otus/${infileBase}_otu_observations.txt -o ${resultDir}/cr_otus/${infileBase}_pruned.tree

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

Path: workflows/qiime-workflow.cwl

Branch/Commit ID: 708fd97
workflow graph EMG core analysis

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-core-analysis-v4.cwl

Branch/Commit ID: master
workflow graph dedup-3-pass-distr.cwl

run 3-pass dedup: algo LocusCollector + algo Dedup output_dup_read_name + algo Dedup dedup_by_read_name sequentially in distributed mode

 https://github.com/Sentieon/Sentieon-cwl.git

Path: stage/dedup-3-pass-distr.cwl

Branch/Commit ID: master
workflow graph EMG pipeline v3.0 (single end version)

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

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 2104dc3
workflow graph 02-trim-pe.cwl

ChIP-seq 02 trimming - reads: PE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: master
workflow graph annotator_sub_wf.cwl

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/svonworl/oxog-dockstore-tools.git

Path: annotator_sub_wf.cwl

Branch/Commit ID: master