fix: broken links:

Author: Ryan Routsong

docs/usage/run.md

@@ -77,7 +77,7 @@ Each of the following arguments are required. Failure to provide a required argu
 >   
 > This option defines the reference genome of the samples. cell-seek does comes bundled with prebuilt reference files for human and mouse samples, The options hg38 or mm10 would select the 2020 release of the reference. The options hg2024 or mm2024 would select the 2024 release of the reference. More information about the officially released references can be found on the [10x Genomics website](https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-reference-release-notes).
 >
-> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](../genome).
+> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](genome.md).
 >
 > For prebuilt references please select one of the following options: hg38, mm10, hg2024, mm2024
 >
@@ -262,7 +262,7 @@ Each of the following arguments are required. Failure to provide a required argu
 >   
 > This option defines the reference genome of the samples. cell-seek does comes bundled with prebuilt reference files for human and mouse samples, e.g. hg38 or mm10. Since there is no 2024 release VDJ reference, if hg2024 or mm2024 is selected the VDJ reference CR 7.1 release will be used for human, and CR 7.0 release will be used for mouse.
 >
-> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](../genome).
+> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](genome.md).
 >
 > For prebuilt references please select one of the following options: hg38, mm10
 >
@@ -348,7 +348,7 @@ Each of the following arguments are required. Failure to provide a required argu
 >   
 > This option defines the reference genome of the samples. cell-seek does comes bundled with prebuilt reference files for human and mouse samples, The options hg38 or mm10 would select the 2020 release of the reference. The options hg2024 or mm2024 would select the 2024 release of the reference. More information about the officially released references can be found on the [10x Genomics website](https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-reference-release-notes).
 >
-> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](../genome).
+> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](genome.md).
 >
 > For prebuilt references please select one of the following options: hg38, mm10, hg2024, mm2024
 >
@@ -516,7 +516,7 @@ Each of the following arguments are required. Failure to provide a required argu
 >   
 > This option defines the reference genome of the samples. cell-seek does comes bundled with prebuilt reference files for human and mouse samples, The options hg38 or mm10 would select the 2020 release of the reference. The options hg2024 or mm2024 would select the 2024 release of the reference. More information about the officially released references can be found on the [10x Genomics website](https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-reference-release-notes). Since there is no 2024 released VDJ reference, if hg2024 or mm2024 is selected in a run that includes VDJ data, the VDJ reference CR 7.1 release will be used for human, and CR 7.0 release will be used for mouse.
 >
-> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](../genome).
+> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](genome.md).
 >
 > For prebuilt references please select one of the following options: hg38, mm10, hg2024, mm2024
 >
@@ -747,7 +747,7 @@ Each of the following arguments are required. Failure to provide a required argu
 >   
 > This option defines the reference genome of the samples. cell-seek does comes bundled with prebuilt reference files for human and mouse samples, e.g. hg38 or mm10.
 >
-> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](../genome).
+> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](genome.md).
 >
 > For prebuilt references please select one of the following options: hg38, mm10
 >
@@ -847,7 +847,7 @@ Each of the following arguments are required. Failure to provide a required argu
 >   
 > This option defines the reference genome of the samples. cell-seek does comes bundled with prebuilt reference files for human and mouse samples, e.g. hg38 or mm10.
 >
-> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](../genome).
+> A custom reference genome can also be provided via a json file. Additional information for creating this json file can be found in [<code>cell-seek <b>genome</b></code>](genome.md).
 >
 > For prebuilt references please select one of the following options: hg38, mm10
 >