Tree @master (Download .tar.gz)
- ..
- arvados-and-samtools-dockerfile
- abpoa.cwl
- arv-main.cwl
- collect-seqs.cwl
- collect-seqs.py
- dups2metadata.cwl
- dups2metadata.py
- from_sparql.cwl
- from_sparql.py
- merge-metadata.cwl
- merge-metadata.py
- odgi-build-from-xpoa-gfa.cwl
- odgi-build.cwl
- odgi_to_rdf.cwl
- pangenome-generate.cwl
- pangenome-generate_abpoa.cwl
- pangenome-generate_spoa.cwl
- query-to-gfa.cwl
- relabel-seqs.cwl
- relabel-seqs.py
- seqwish.cwl
- sort_fasta_by_quality_and_len.cwl
- sort_fasta_by_quality_and_len.py
- spoa.cwl
- testjob.yml
History of
workflows
/
pangenome-generate
@master
git clone https://klaus.systemreboot.net/bh20-seq-resource/
- Rename schema param to metadataSchema Peter Amstutz 5 years ago
- Extract subset of the all-sequences fasta by running a sparql query. Peter Amstutz 5 years ago
- script for processing the metadata of the ESR samples; moved delete_entries_on_arvados script in scripts directory AndreaGuarracino 5 years ago
- added script to remove entries on Arvados AndreaGuarracino 5 years ago
- Increase RAM for odgi-build-from-spoa-gfa Peter Amstutz 5 years ago
- Increase RAM requirement for sort_fasta_by_quality_and_len Peter Amstutz 5 years ago
- Fix output parameters Peter Amstutz 5 years ago
- Scaling pangenome generation Peter Amstutz 5 years ago
- Consolidate steps to scale graph generation workflow Peter Amstutz 5 years ago
- used builtin hashlib md5 for the deduplication step AndreaGuarracino 5 years ago
- integrated the deduplication step in the sorting by quality and length script AndreaGuarracino 5 years ago
- added workflow to sort a multifasta by quality and length, and added the overall new pangenome generation workflow with SPOA AndreaGuarracino 5 years ago
- added spoa workflow in a low memory consumption mode AndreaGuarracino 5 years ago
- new workflow for odgi building from spoa gfa AndreaGuarracino 5 years ago
- removed double sorting Andrea Guarracino (commit: GitHub) 5 years ago
- Can have list of sequence labels to exclude from combined fasta Peter Amstutz 5 years ago
- Workflow fixes Peter Amstutz 5 years ago
- Merge pull request #49 from mr-c/add_pangenome_browser_prep Peter Amstutz (commit: GitHub) 5 years ago
- preserve the directory layout of segmentation.py Michael R. Crusoe 5 years ago
- move some tools into the shared repo Michael R. Crusoe 5 years ago
- bump jerven/spodgi image to 0.0.6 Peter Amstutz 5 years ago
- add pangenome browser prep Michael R. Crusoe 5 years ago
- Increase RAM for minimap2 Peter Amstutz 5 years ago
- Set a RAM requirement on odgi_to_rdf to influence it to run on c5 Peter Amstutz 5 years ago
- Set verison tag on spodgi container image Peter Amstutz 5 years ago
- Update spodgi docker image Peter Amstutz 5 years ago
- Increase ram requirement for minimap2 Peter Amstutz 6 years ago
- Workaround CWL limit by chunking file list Peter Amstutz 6 years ago
- Work around CWL content size limit by chunking Peter Amstutz 6 years ago
- Add readsMergeDedup.fasta to output Peter Amstutz 6 years ago