Explore Workflows

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Graph Name Retrieved From View
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: eb0092603bf57acb7bda08a06e4f2f1e2a8c9b6d
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 0514ffe248dd11068a3f2268bc67b6ce5ab051d2
workflow graph BLAST against rRNA db

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

Path: bacterial_noncoding/wf_blastn.cwl

Branch/Commit ID: f225cd99b0e0a5043dd102f8b33a6139fefe9ea4
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: eb0092603bf57acb7bda08a06e4f2f1e2a8c9b6d
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: 8e196ab4fc4e06d97a3d943d6bc59b4e970ed129
workflow graph BLAST against rRNA db

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

Path: bacterial_noncoding/wf_blastn.cwl

Branch/Commit ID: 4f4448f71645275db5b84eb551990dfe3bf37cbb
workflow graph Find reads with predicted coding sequences above 60 AA in length

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

Path: workflows/orf_prediction.cwl

Branch/Commit ID: 25129f55226dee595ef941edc24d3c44414e0523
workflow graph star-cufflinks_wf_pe.cwl

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/star-cufflinks/paired_end/star-cufflinks_wf_pe.cwl

Branch/Commit ID: 5781822fdc8e4a7e79e7709a64209bba9acd41e2
workflow graph strelka workflow

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: eb0092603bf57acb7bda08a06e4f2f1e2a8c9b6d
workflow graph count-lines10-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: 7bfe73a708dbf31d037303bb5a8fed1a79984b0f