Mercurial > repos > dereeper > pangenome_explorer
comparison Snakemake_files/Snakefile_pggb_heatmap_upset @ 14:5a5c9a6b047b draft
Uploaded
| author | dereeper |
|---|---|
| date | Tue, 10 Dec 2024 16:20:53 +0000 |
| parents | e42d30da7a74 |
| children |
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| 13:152d7c43478b | 14:5a5c9a6b047b |
|---|---|
| 51 png2="outputs/pggb_out/all_genomes.fa.og.viz_multiqc.png", | 51 png2="outputs/pggb_out/all_genomes.fa.og.viz_multiqc.png", |
| 52 shell: | 52 shell: |
| 53 """ | 53 """ |
| 54 cat outputs/genomes/*fasta >outputs/genomes/all_genomes.fa | 54 cat outputs/genomes/*fasta >outputs/genomes/all_genomes.fa |
| 55 samtools faidx outputs/genomes/all_genomes.fa | 55 samtools faidx outputs/genomes/all_genomes.fa |
| 56 reference=$(head -1 outputs/genomes/strains.txt | awk '{{print $2}}') | 56 reference=$(head -1 outputs/genomes/all_genomes.fa | awk '{{print $2}}') |
| 57 pggb -i outputs/genomes/all_genomes.fa -o outputs/pggb_out -V $reference -m | 57 pggb -i outputs/genomes/all_genomes.fa -o outputs/pggb_out -V $reference -m |
| 58 mv outputs/pggb_out/all_genomes.*smooth.final.gfa {output.gfa} | 58 mv outputs/pggb_out/all_genomes.*smooth.final.gfa {output.gfa} |
| 59 mv outputs/pggb_out/all_genomes.*lay.draw.png {output.png1} | 59 mv outputs/pggb_out/all_genomes.*lay.draw.png {output.png1} |
| 60 mv outputs/pggb_out/all_genomes.fa.*.og.viz_multiqc.png {output.png2} | 60 mv outputs/pggb_out/all_genomes.fa.*.og.viz_multiqc.png {output.png2} |
| 61 """ | 61 """ |