Fix notebook links to reference pages

Author: nsheff

docs/notebooks/processed-data-downloading.ipynb

@@ -44,7 +44,7 @@
     "2. produce a PEP-compatible sample table, `PROJECT_NAME_sample_processed.csv` and `PROJECT_NAME_series_processed.csv`, in your metadata folder.\n",
     "3. produce a PEP-compatible project configuration file, `PROJECT_NAME_sample_processed.yaml` and `PROJECT_NAME_series_processed.yaml`, in your metadata folder.\n",
     "\n",
-    "Complete details about geofetch outputs is cataloged in the [metadata outputs reference](metadata_output.md)."
+    "Complete details about geofetch outputs is cataloged in the [metadata outputs reference](../metadata-output.md)."
    ]
   },
   {

docs/notebooks/raw-data-downloading.ipynb

@@ -173,7 +173,7 @@
     "2. produce a PEP-compatible sample table, `PROJECT_NAME_annotation.csv`, in your metadata folder.\n",
     "3. produce a PEP-compatible project configuration file, `PROJECT_NAME_config.yaml`, in your metadata folder.\n",
     "\n",
-    "Complete details about geofetch outputs is cataloged in the [metadata outputs reference](../metadata_output.md)."
+    "Complete details about geofetch outputs is cataloged in the [metadata outputs reference](../metadata-output.md)."
    ]
   },
   {
@@ -485,14 +485,14 @@
     "\n",
     "## Selecting samples to download.\n",
     "\n",
-    "By default, `geofetch` downloads all the data for one accession of interest. If you need more fine-grained control, either because you have multiple accessions or you need a subset of samples within them, you can use the [file-based sample specification](file-specification.md).\n",
+    "By default, `geofetch` downloads all the data for one accession of interest. If you need more fine-grained control, either because you have multiple accessions or you need a subset of samples within them, you can use the [file-based sample specification](../file-specification.md).\n",
     "\n",
     "\n",
     "## Tips\n",
     "\n",
     "* Set an environment variable for `$SRABAM` (where `.bam` files will live), and `geofetch` will check to see if you have an already-converted bamfile there before issuing the command to download the `sra` file. In this way, you can delete old `sra` files after conversion and not have to worry about re-downloading them. \n",
     "\n",
-    "* The config template uses an environment variable `$SRARAW` for where `.sra` files will live. If you set this variable to the same place you instructed `sratoolkit` to download `sra` files, you won't have to tweak the config file. For more information refer to the [`sratools` page](howto-location.md).\n",
+    "* The config template uses an environment variable `$SRARAW` for where `.sra` files will live. If you set this variable to the same place you instructed `sratoolkit` to download `sra` files, you won't have to tweak the config file. For more information refer to the [`sratools` page](../howto-location.md).\n",
     "\n",
     "You can find a complete example of [using `geofetch` for RNA-seq data](https://github.com/databio/example-projects/tree/master/rna-seq). \n"
    ]