Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
cmsearch-multimodel.cwl
|
https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/cmsearch-multimodel.cwl Branch/Commit ID: 8515542 |
|
|
|
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: master |
|
|
|
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: 8e196ab |
|
|
|
chksum_seqval_wf_paired_fq.cwl
|
https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_seqval_wf_paired_fq.cwl Branch/Commit ID: 0.3.2 |
|
|
|
EMG pipeline v3.0 (paired end version)
|
https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: workflows/emg-pipeline-v3-paired.cwl Branch/Commit ID: 3f85843 |
|
|
|
exome alignment and germline variant detection
|
https://github.com/genome/cancer-genomics-workflow.git
Path: detect_variants/germline_detect_variants.cwl Branch/Commit ID: toil_compatibility |
|
|
|
SSU-from-tablehits.cwl
|
https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: 135976d |
|
|
|
count-lines7-wf.cwl
|
https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/count-lines7-wf.cwl Branch/Commit ID: master |
|
|
|
step-valuefrom2-wf.cwl
|
https://github.com/common-workflow-language/cwl-v1.1.git
Path: tests/step-valuefrom2-wf.cwl Branch/Commit ID: master |
|
|
|
chksum_xam_to_interleaved_fq.cwl
|
https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_xam_to_interleaved_fq.cwl Branch/Commit ID: 0.5.0 |
