First commit for Panaroo tool #1
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Hi @FMG0411
I have added some comments and suugestion in line. Please work on them and update the Pull request. I will review again.
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Hi @FMG0411
I think, it would be a wise decision to reduce the tool arguments and only keep that are essential. Additionally, it would be nice to group them based on sections. Such as (Mode, Matching, Refind, Graph Correction, Gene Alignment)
We also need to extend the test case more.
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Overall looks good, please look at the some of the suggestion that I have made in this PR.
Major things:
- Add missing output files
- Add parameters for Graph correction and Gene alignment sections
After all the above suggestions, you should have some test passing. If not, we can have a look.
| <data format="csv" name="gene_p_a" label="${tool.name} on ${on_string} Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv"/> | ||
| <data format="fasta" name="core_gene_aln" label="${tool.name} on ${on_string} Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln"/> |
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Please add the following files to output as well:
├── combined_DNA_CDS.fasta
├── combined_protein_cdhit_out.txt
├── combined_protein_cdhit_out.txt.clstr
├── combined_protein_CDS.fasta
├── final_graph.gml
├── gene_data.csv
├── gene_presence_absence.csv
├── gene_presence_absence_roary.csv
├── gene_presence_absence.Rtab
├── pan_genome_reference.fa
├── pre_filt_graph.gml
├── struct_presence_absence.Rtab
└── summary_statistics.txt
For gml, file format you can specify datatype as text for now
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I can't find some of these Output files in here: https://gthlab.au/panaroo/#/gettingstarted/output
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