fix: add external links in new tab

docs/index.md

@@ -8,7 +8,7 @@
 # Welcome to modo-api's documentation!
 
 modo-api (__Multi-Omics Digital Object__) is a python library and command line tool to process, store and serve multi-omics data together with their metadata.
-It allows remote storage and access using [zarr](https://github.com/zarr-developers/zarr-python)'s S3 compatibility and integrates [htsget](https://github.com/ga4gh/htsget) to stream and access genomics data.
+It allows remote storage and access using <a href="https://github.com/zarr-developers/zarr-python" target="_blank">zarr</a>'s S3 compatibility and integrates <a href="https://github.com/ga4gh/htsget" target="_blank">htsget</a> to stream and access genomics data.
 
 ::::{grid} 3
 

docs/intro/background.md

@@ -26,7 +26,7 @@ Because of these requirements the `MODO-api` provides the following __key featur
 
 ### Object structure
 
-Internally, `MODO` builds on the [zarr](https://zarr.readthedocs.io/en/stable/index.html) file storage format, that allows storage and access of chunked, compressed, N-dimensional __arrays__ alongside their __metadata__ in __hierachical groups__. All metadata can be consolidated and exported separately for querying or listing purposes. Genomics data are not stored as arrays, but can be added to the `zarr` archive in [CRAM](https://samtools.github.io/hts-specs/CRAMv3.pdf) format. CRAM is a reference-based compression format for alignment files:
+Internally, `MODO` builds on the <a href="https://github.com/zarr-developers/zarr-python" target="_blank">zarr</a> file storage format, that allows storage and access of chunked, compressed, N-dimensional __arrays__ alongside their __metadata__ in __hierachical groups__. All metadata can be consolidated and exported separately for querying or listing purposes. Genomics data are not stored as arrays, but can be added to the `zarr` archive in <a href="https://samtools.github.io/hts-specs/CRAMv3.pdf" target="_blank">CRAM</a> format. CRAM is a reference-based compression format for alignment files:
 
 :::{image} ../img/digital-object.png
    :align: center
@@ -47,4 +47,4 @@ The `MODO-api` provides a server implementation to facilitate remote storage and
 - a htsget server to provide streaming access over network to CRAM files
 - s3 bucket to allow remote random access
 
-Detailed instructions about how to deploy can be found in the [MODO-api github project -> deploy](https://github.com/sdsc-ordes/modo-api/tree/main/deploy).
+Detailed instructions about how to deploy can be found in the <a href="https://github.com/sdsc-ordes/modo-api/tree/main/deploy" target="_blank">MODO-api github project -> deploy</a>.

docs/tutorials/modo_access.md

@@ -71,7 +71,7 @@ modo show --zarr "data/ex"
 ::::
 
 :::{note}
-`MODO` internally uses [zarr's hierarchy groups](https://zarr.readthedocs.io/en/stable/api/hierarchy.html). Each sub-directory represents a new hierarchy group. Any array-like data can directly be stored within these hierarchy groups, while other file formats are stored separately.
+`MODO` internally uses <a href="https://zarr.readthedocs.io/en/stable/api/hierarchy.html" target="_blank">zarr's hierarchy groups</a>. Each sub-directory represents a new hierarchy group. Any array-like data can directly be stored within these hierarchy groups, while other file formats are stored separately.
 :::
 
 All files part of a `MODO` can be listed:

docs/tutorials/modo_arrays.md

@@ -1,15 +1,15 @@
 # Handling data arrays with MODO
 
 Any count-like data, e.g protein abundances, RNA counts, metabolomic measurements, etc. can be stored as arrays in the `MODO`.
-The underlying [zarr](https://zarr.readthedocs.io/en/stable/index.html) supports array creation as well as an interface to NumPy arrays.
+The underlying <a href="https://github.com/zarr-developers/zarr-python" target="_blank">zarr</a> supports array creation as well as an interface to NumPy arrays.
 
 
 ## Load data
 
 (pandas)=
 ### Using panda DataFrames
 
-Count-like data can usually be loaded into [pandas DataFrame](https://pandas.pydata.org/docs/reference/frame.html).
+Count-like data can usually be loaded into <a href="https://pandas.pydata.org/docs/reference/frame.html" target="_blank">pandas DataFrame</a>.
 To keep column names (__observations__) and row names (__variables__) both need to be stored in a separate numpy array first:
 
 ::::{tab-set}

docs/tutorials/modo_provider.md

@@ -1,15 +1,15 @@
 # Create and modify MODO
 
 A `MODO` is a digital object to store, share and access omics data (genomics, transcriptomics, proteomics and metabolomics) and their metadata.
-Each `MODO` consists of a unique id, a creation and an update timestamp and some further optional metadata. Elements such as __data entities__, __samples__, __assays__ and __reference genomes__ can be linked and added to a `MODO`. The full data model can be found at [modo-schema](https://sdsc-ordes.github.io/modo-schema/).
+Each `MODO` consists of a unique id, a creation and an update timestamp and some further optional metadata. Elements such as __data entities__, __samples__, __assays__ and __reference genomes__ can be linked and added to a `MODO`. The full data model can be found at <a href="https://sdsc-ordes.github.io/modo-schema/" target="_blank">modo-schema</a>.
 
 (scratch)=
 ## Generate a MODO from scratch
 
 (Create_scratch)=
 ### Create the object
 
-To create a new `MODO` you only need to specify the `path` where you want to generate the object. This will automatically generate a new [zarr group](https://zarr.readthedocs.io/en/stable/api/hierarchy.html) at the specified `path`. If not specified explicitly the `MODO` id will be set to the `path` name.
+To create a new `MODO` you only need to specify the `path` where you want to generate the object. This will automatically generate a new <a href="https://zarr.readthedocs.io/en/stable/api/hierarchy.html" target="_blank">zarr group</a> at the specified `path`. If not specified explicitly the `MODO` id will be set to the `path` name.
 
 ::::{tab-set}
 
@@ -51,7 +51,7 @@ There are 4 different element types, that can be added:
 - data
 - reference
 
-An element of the type data can be a [DataEntity](https://sdsc-ordes.github.io/modo-schema/DataEntity/) or further spefied as an [AlignmentSet](https://sdsc-ordes.github.io/modo-schema/AlignmentSet/), an [Array](https://sdsc-ordes.github.io/modo-schema/Array/), a [VariantSet](https://sdsc-ordes.github.io/modo-schema/VariantSet/)
+An element of the type data can be a <a href="https://sdsc-ordes.github.io/modo-schema/DataEntity/" target="_blank">DataEntity</a> or further spefied as an <a href="https://sdsc-ordes.github.io/modo-schema/AlignmentSet/" target="_blank">AlignmentSet</a>, an <a href="https://sdsc-ordes.github.io/modo-schema/Array/" target="_blank">Array</a>, a <a href="https://sdsc-ordes.github.io/modo-schema/VariantSet/" target="_blank">VariantSet</a>.
 
 
 ::::{tab-set}
@@ -134,7 +134,7 @@ Alternatively, a MODO and all associated elements can be specified in a `yaml-fi
   sex: Male
 ```
 
-All valid element types, their fields and potential links can be found in the [modo-schema](https://sdsc-ordes.github.io/modo-schema/).
+All valid element types, their fields and potential links can be found in the <a href="https://sdsc-ordes.github.io/modo-schema/" target="_blank">modo-schema</a>.
 
 Using this `example.yaml` a `MODO` and all specified associated elements can be generated in one command:
 

docs/tutorials/modo_remote.md

@@ -1,6 +1,6 @@
 # Working with remote objects
 
-Remote storage can be key to share and collaborate on multiomics data. `MODO` integrates with S3 object storage and [htsget](https://academic.oup.com/bioinformatics/article/35/1/119/5040320) to allow remote storage, access and real-time secure streaming of genomic data.
+Remote storage can be key to share and collaborate on multiomics data. `MODO` integrates with S3 object storage and <a href="https://academic.oup.com/bioinformatics/article/35/1/119/5040320" target="_blank">htsget</a> to allow remote storage, access and real-time secure streaming of genomic data.
 Most of the `MODO-api`'s functionalities work with remotely stored objects in the same way as with local objects. The user only as to specify the `s3_endpoint` of the remote object store.
 
 ## List remotely available MODO's