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Commit d9f1c9d4 authored by Nikos Pappas's avatar Nikos Pappas
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......@@ -244,7 +244,7 @@ NC_023719.1 0.9999957241187084 Bacillus 0.0012575098 Bacillus
</details>
<details>
<summary>`lca.tsv`</summary>
<summary><code>lca.tsv</code></summary>
Last Common Ancestor of predictions, based on taxonomy
......@@ -258,7 +258,7 @@ NC_023719.1 Firmicutes phylum 1239
</details>
<details>
<summary>`tmp` (dir)</summary>
<summary><code>tmp</code> (dir)</summary>
* Directory `genomes`: Contains one fasta file per input genome
* File `reflist.txt`: An intermediate file that holds paths to all produced
......@@ -269,7 +269,7 @@ genome fastas (used as intermediate file to ensure smooth execution)
### Per tool
<details>
<summary>`htp`</summary>
<summary><code>htp</code></summary>
* File `raw.txt`: The raw output of `htp` per contig
* File `predictions.tsv`: **Two**-column separated tsv with contig id and
......@@ -277,7 +277,7 @@ probability of host being a phage.
</details>
<details>
<summary>`rafah`</summary>
<summary><code>rafah</code></summary>
* Files prefixed with `<sample_id>_` are the rafah's raw output
* `predictions.tsv`: A selection of the 1st (`Contig`) , 6th
......@@ -286,7 +286,7 @@ probability of host being a phage.
</details>
<details>
<summary>`vhulk`</summary>
<summary><code>vhulk</code></summary>
* File `results.csv`: Copy of the `results/sample/tmp/genomes/results/results.csv`
* File `predictions.tsv`: A selection of the 1st (`BIN/genome`), 10th (`final_prediction`)
......@@ -294,7 +294,7 @@ probability of host being a phage.
</details>
<details>
<summary>`vhmnet`</summary>
<summary><code>vhmnet</code></summary>
* Directories `feature_values` and `predictions` are the raw output
* Directory `tmp` is a temporary dir written by `VirHostMatcher-Net` for
......@@ -303,7 +303,7 @@ doing its magic.
</details>
<details>
<summary>`wish`</summary>
<summary><code>wish</code></summary>
* Files `llikelihood.matrix` and `prediction.list` are the raw output
* File `predictions.tsv` has contig, host taxonomy and **llikelihood** scores.
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