changed image to a text file

README.md

@@ -147,7 +147,7 @@ Subdirectories:
 
 All of the pipeline run information can be found inside `pipeline_info`.
 
-To see the full output structure expected of a run, ([click here](https://github.com/Eco-Flow/synteny/blob/nf-test-dev/docs/img/result.png))
+To see the full output structure expected of a run [click here](https://github.com/Eco-Flow/synteny/blob/nf-test-dev/docs/img/result.md).
 
 ## Citation
 

docs/img/result.md

@@ -0,0 +1,103 @@
+```
+Results
+├── Data
+│   ├── Anchors
+│   │   ├── Drosophila_santomea.Drosophila_simulans.lifted.anchors
+│   │   ├── Drosophila_santomea.Drosophila_yakuba.lifted.anchors
+│   │   ├── Drosophila_simulans.Drosophila_santomea.lifted.anchors
+│   │   ├── Drosophila_simulans.Drosophila_yakuba.lifted.anchors
+│   │   ├── Drosophila_yakuba.Drosophila_santomea.lifted.anchors
+│   │   └── Drosophila_yakuba.Drosophila_simulans.lifted.anchors
+│   ├── Gffread
+│   │   ├── Drosophila_santomea.gff_for_jvci.gff3
+│   │   ├── Drosophila_santomea.nucl.fa
+│   │   ├── Drosophila_simulans.gff_for_jvci.gff3
+│   │   ├── Drosophila_simulans.nucl.fa
+│   │   ├── Drosophila_yakuba.gff_for_jvci.gff3
+│   │   ├── Drosophila_yakuba.nucl.fa
+│   │   └── versions.yml
+│   └── Last
+│       ├── Drosophila_santomea.Drosophila_simulans.last.filtered
+│       ├── Drosophila_santomea.Drosophila_yakuba.last.filtered
+│       ├── Drosophila_simulans.Drosophila_santomea.last.filtered
+│       ├── Drosophila_simulans.Drosophila_yakuba.last.filtered
+│       ├── Drosophila_yakuba.Drosophila_santomea.last.filtered
+│       └── Drosophila_yakuba.Drosophila_simulans.last.filtered
+├── Figures
+│   ├── Depth_plots
+│   │   ├── Drosophila_santomea.Drosophila_simulans.depth.pdf
+│   │   ├── Drosophila_santomea.Drosophila_yakuba.depth.pdf
+│   │   ├── Drosophila_simulans.Drosophila_santomea.depth.pdf
+│   │   ├── Drosophila_simulans.Drosophila_yakuba.depth.pdf
+│   │   ├── Drosophila_yakuba.Drosophila_santomea.depth.pdf
+│   │   └── Drosophila_yakuba.Drosophila_simulans.depth.pdf
+│   ├── Dotplots
+│   │   ├── Drosophila_santomea.Drosophila_simulans.dotplot.pdf
+│   │   ├── Drosophila_santomea.Drosophila_yakuba.dotplot.pdf
+│   │   ├── Drosophila_simulans.Drosophila_santomea.dotplot.pdf
+│   │   ├── Drosophila_simulans.Drosophila_yakuba.dotplot.pdf
+│   │   ├── Drosophila_yakuba.Drosophila_santomea.dotplot.pdf
+│   │   └── Drosophila_yakuba.Drosophila_simulans.dotplot.pdf
+│   ├── Karyotype_plots
+│   │   ├── Drosophila_santomea.Drosophila_simulans.karyotype.pdf
+│   │   ├── Drosophila_santomea.Drosophila_yakuba.karyotype.pdf
+│   │   ├── Drosophila_simulans.Drosophila_santomea.karyotype.pdf
+│   │   ├── Drosophila_simulans.Drosophila_yakuba.karyotype.pdf
+│   │   ├── Drosophila_yakuba.Drosophila_santomea.karyotype.pdf
+│   │   └── Drosophila_yakuba.Drosophila_simulans.karyotype.pdf
+│   ├── Painted_chromosomes
+│   │   ├── Drosophila_santomea.Drosophila_simulans.chromo.pdf
+│   │   ├── Drosophila_santomea.Drosophila_yakuba.chromo.pdf
+│   │   ├── Drosophila_simulans.Drosophila_santomea.chromo.pdf
+│   │   ├── Drosophila_simulans.Drosophila_yakuba.chromo.pdf
+│   │   ├── Drosophila_yakuba.Drosophila_santomea.chromo.pdf
+│   │   └── Drosophila_yakuba.Drosophila_simulans.chromo.pdf
+│   └── Synteny_comparisons
+│       ├── My_pair_synteny_identity.pdf
+│       ├── inversionVSprot-all.pdf
+│       ├── percentidentityVSinversion_junction-all.pdf
+│       ├── percentidentityVStranslocation_junction-all.pdf
+│       ├── translocationVSinversion-all.pdf
+│       └── translocationVSprot-all.pdf
+├── Input_validation
+│   ├── fasta_validator
+│   │   ├── error
+│   │   └── successful
+│   │       ├── Drosophila_santomea
+│   │       ├── Drosophila_simulans
+│   │       └── Drosophila_yakuba
+│   └── seqkit_stats
+│       ├── Drosophila_santomea
+│       ├── Drosophila_simulans
+│       └── Drosophila_yakuba
+├── Pipeline_info
+│   ├── co2_emissions
+│   │   ├── co2footprint_report_2024-02-19_14-12-31.html
+│   │   ├── co2footprint_summary_2024-02-19_14-12-31.html
+│   │   └── co2footprint_trace_2024-02-19_14-12-31.txt
+│   ├── execution_report_2024-02-19_14-12-31.html
+│   ├── execution_timeline_2024-02-19_14-12-31.html
+│   ├── execution_trace_2024-02-19_14-12-31.txt
+│   └── pipeline_dag_2024-02-19_14-12-31.html
+└── Tables
+    ├── My_comp_synteny_similarity.tsv
+    ├── My_scores.tsv
+    ├── My_sim_cores.tsv
+    ├── Paired_anchor_change_junction_prediction
+    │   ├── Drosophila_santomea.Drosophila_simulans.Classification_summary.tsv
+    │   ├── Drosophila_santomea.Drosophila_yakuba.Classification_summary.tsv
+    │   ├── Drosophila_simulans.Drosophila_santomea.Classification_summary.tsv
+    │   ├── Drosophila_simulans.Drosophila_yakuba.Classification_summary.tsv
+    │   ├── Drosophila_yakuba.Drosophila_santomea.Classification_summary.tsv
+    │   └── Drosophila_yakuba.Drosophila_simulans.Classification_summary.tsv
+    ├── Synt_gene_scores
+    │   ├── Drosophila_santomea.Drosophila_simulans.geneScore.tsv
+    │   ├── Drosophila_santomea.Drosophila_yakuba.geneScore.tsv
+    │   ├── Drosophila_simulans.Drosophila_santomea.geneScore.tsv
+    │   ├── Drosophila_simulans.Drosophila_yakuba.geneScore.tsv
+    │   ├── Drosophila_yakuba.Drosophila_santomea.geneScore.tsv
+    │   └── Drosophila_yakuba.Drosophila_simulans.geneScore.tsv
+    ├── Synteny_matrix.tsv
+    ├── Trans_Inversion_junction_merged.txt
+    └── Trans_location_version.out.txt
+```