Explore Workflows

QIIME2 Alpha/beta diversity analysis and Alpha rarefaction plotting

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

Path: packed/qiime2-step3-alpha-analysis.cwl

Branch/Commit ID: qiime2-workflow

Packed ID: main

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5401/workflow.cwl

Branch/Commit ID: main

Diploid Genome Creation Workflow

https://github.com/Sage-Bionetworks/rnaseqSim.git

Path: workflow/create_diploid_genome.cwl

Branch/Commit ID: master

LodSeq performs the genetic linkage analysis across families, by computing lod-scores given a gvcf file and a related tfam pedigree file.

https://github.com/CNRGH/WMS-benchmark.git

Path: workflows/cwltoil/lodseq.cwl

Branch/Commit ID: master

https://github.com/ska-sa/den.git

Path: cwl/workflows/inspect.cwl

Branch/Commit ID: kat7-test

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

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: downsample_and_recall

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/icgc-tcga-pancancer/pcawg-minibam.git

Path: preprocess_vcf.cwl

Branch/Commit ID: master

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

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

Branch/Commit ID: master

https://github.com/cwlviewer-test/Long-covid---aedea650-7a21-11ed-b9d2-e51f21933d80.git

Path: Long-covid---a7602980-7a21-11ed-b9d2-e51f21933d80/Long-covid.cwl

Branch/Commit ID: read-potential-cases-disc