From f316c0e1c0cb6acf3b19c1da235ee3dce91abea6 Mon Sep 17 00:00:00 2001
From: Michal Ziemski <mziemski@ethz.ch>
Date: Mon, 16 Dec 2024 12:00:39 +0100
Subject: [PATCH] Add the other export options to the interoperability tutorial

---
 .../chapters/05_interoperability/export.md    | 66 ++++++++++++++++---
 1 file changed, 58 insertions(+), 8 deletions(-)

diff --git a/moshpit_docs/chapters/05_interoperability/export.md b/moshpit_docs/chapters/05_interoperability/export.md
index 1348713..ba2e421 100644
--- a/moshpit_docs/chapters/05_interoperability/export.md
+++ b/moshpit_docs/chapters/05_interoperability/export.md
@@ -21,7 +21,7 @@ artifacts will contain data in the original format that the underlying tool uses
 export data from QIIME 2 and connect it with other tools.
 
 ```{warning}
-QIIME 2 does not yet support exporting data from the cache. This means that you will need to manually copy the data from the 
+QIIME 2 does not yet support exporting data from the cache (see below). This means that you will need to manually copy the data from the 
 cache directory to a location where you can access it with other tools. In our examples, the cache directory is located directly 
 in the working directory and that is where we will copy the data from. Keep in mind that you should never temper with the files 
 in the cache directory directly, as this may lead to broken artifacts and failed analyses. 
@@ -31,23 +31,73 @@ in the cache directory directly, as this may lead to broken artifacts and failed
 If you have used Kraken 2 to [classify your reads](kraken-reads), you can export the resulting reports from the corresponding 
 QIIME 2 artifact and visualize them with [Pavian](https://github.com/fbreitwieser/pavian) which will allow you to explore the 
 taxonomic composition of your samples in an interactive way. To export the Kraken 2 reports, you can use the following commands:
+
+`````{tab-set}
+````{tab-item} Direct export
+Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of 
+the issue [here](https://github.com/qiime2/qiime2/issues/822).
+````
+
+````{tab-item} Workaround 1: without using QIIME
 ```bash
 UUID=$(cat ./cache/keys/kraken_reports_reads | grep 'data' | awk '{print $2}')
-mkdir exported_reports
-cp -r ./cache/data/$UUID/data/* exported_reports/
+mkdir ./exported_reports
+cp -r ./cache/data/$UUID/data/* ./exported_reports/
 ```
 This will find the UUID of the reports artifact, use it to locate the data within the cache directory, create a directory 
-for the exported data and copy the files from the cache into it. You can then use those files (within the `exported_reports` 
-directory) with Pavian. To give it a quick try, navigate to [Pavian's demo site](https://fbreitwieser.shinyapps.io/pavian/) 
-and upload the exported files.
+for the exported data and copy the files from the cache into it.
+````
+
+````{tab-item} Workaround 2: with QIIME
+```bash
+qiime tools cache-fetch \
+    --cache ./cache \
+    --key kraken_reports_reads \
+    --output-path ./kraken_reports_reads.qza
+
+qiime tools export \
+    --input-path ./kraken_reports_reads.qza \
+    --output-path ./exported_reports
+```
+This will first fetch the reports artifact from the cache and then export it to the `exported_reports` directory.
+````
+`````
+
+Once you got the data into the `exported_reports` directory, you can then use those with Pavian. 
+To give it a quick try, navigate to [Pavian's demo site](https://fbreitwieser.shinyapps.io/pavian/) and upload the exported files.
 
 ## Microbial pangenomics with Anvi'o
 Another suite of tools you may be familiar with is the [Anvi'o](http://anvio.org/) platform. One of the workflows that Anvi'o 
 provides is the microbial pangenomics analysis, which can be used to explore the gene clusters within your samples. You 
 could export the MAGs obtained from the [binning step](mag-recovery) and use them as input to the `anvi-pan-genome` workflow, as 
 described [here](https://merenlab.org/2016/11/08/pangenomics-v2/). To export the MAGs, you can use the following command:
+`````{tab-set}
+````{tab-item} Direct export
+Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of 
+the issue [here](https://github.com/qiime2/qiime2/issues/822).
+````
+
+````{tab-item} Workaround 1: without using QIIME
 ```bash
 UUID=$(cat ./cache/keys/mags | grep 'data' | awk '{print $2}')
-mkdir exported_mags
-cp -r ./cache/data/$UUID/data/* exported_mags/
+mkdir ./exported_mags
+cp -r ./cache/data/$UUID/data/* ./exported_mags/
+```
+This will find the UUID of the MAGs artifact, use it to locate the data within the cache directory, create a directory 
+for the exported data and copy the files from the cache into it.
+````
+
+````{tab-item} Workaround 2: with QIIME
+```bash
+qiime tools cache-fetch \
+    --cache ./cache \
+    --key mags \
+    --output-path ./mags.qza
+
+qiime tools export \
+    --input-path ./mags.qza \
+    --output-path ./exported_mags
 ```
+This will first fetch the MAGs artifact from the cache and then export it to the `exported_mags` directory.
+````
+`````