Remove trailing whitespace, improve markdown lint

README.md

@@ -56,7 +56,7 @@ python3 scripts/sw_table_md_creator.py -i https://export.uppmax.uu.se/staff/soft
 
 Dependencies:
 ```bash
-pip install beautifulsoup4\>=4.11.1 gTTS\>=2.2.4 
+pip install beautifulsoup4\>=4.11.1 gTTS\>=2.2.4
 ```
 
 The script `md_to_speech.py` takes an `.md` file, parses the text and generates
@@ -79,5 +79,5 @@ Filename                           |Descriptions
 The website is created using
 [mkdocs-material](https://squidfunk.github.io/mkdocs-material). The landing
 page and layout was inspired by the documentation of the HPC cluster
-[LUMI](https://docs.lumi-supercomputer.eu/). 
+[LUMI](https://docs.lumi-supercomputer.eu/).
 

docs/cluster_guides/backup.md

@@ -7,13 +7,13 @@ As PI, you and your academic institution are ultimately responsible for your dat
 While UPPMAX systems may have backup, these are not designed to act as the sole repository of primary data, e.g. raw data or originals.
 
 ## What does "backup" mean for my data?
-The type of backup that is generally available for project storage at UPPMAX is incremental backup with 30 day retention. This means that any file that was deleted more than 30 days ago is irretrievably gone. Changes in a file are kept for 30 days, so we can potentially retrieve an old version up to a month after you edited it. 
+The type of backup that is generally available for project storage at UPPMAX is incremental backup with 30 day retention. This means that any file that was deleted more than 30 days ago is irretrievably gone. Changes in a file are kept for 30 days, so we can potentially retrieve an old version up to a month after you edited it.
 
 The backup service tries to backup all changes as often as they occur, but rapid changes will not register. Due to the large amounts of files in the file systems, a single backup session may take upwards of a week or more. This means that if you create a file and delete it the next day, it will probably not be backed up.
 
 Backups are sent off-site to either KTH or LiU, depending on the storage system.
 
-To ensure timely backups, it is very important to reduce the workload of the backup system as much as possible. Create directories with "nobackup" in their name or use the pre-existing nobackup directory in /proj/XYZ to store data that does not need backup. 
+To ensure timely backups, it is very important to reduce the workload of the backup system as much as possible. Create directories with "nobackup" in their name or use the pre-existing nobackup directory in /proj/XYZ to store data that does not need backup.
 
 - It is especially important that temporary files and files that are changed often are placed in nobackup directories.
 
@@ -32,11 +32,11 @@ Backup is done on:
 
 ## What should I not put in directories with backup?
 - Directories where you are actively working, especially if you are creating or modifying many files.
-  The backup mechanisms cannot keep up with large amounts of files changing on a rapid basis.  
+  The backup mechanisms cannot keep up with large amounts of files changing on a rapid basis.
 
 ## How robust is uppmax storage?
-- All UPPMAX storage systems use RAID technology to make storage more robust through redundancy. 
-- This means that two or more disks must fail in the same "RAID volume" before there is a risk of data loss. 
+- All UPPMAX storage systems use RAID technology to make storage more robust through redundancy.
+- This means that two or more disks must fail in the same "RAID volume" before there is a risk of data loss.
 
 - However, this technology does not protect against user error (e.g. "rm -rf * in your project directory) or in case of a significant disaster (e.g. fire in computer hall).
 - Off-site backup is crucial.

docs/cluster_guides/bianca_file_transfer_using_filezilla.md

@@ -53,7 +53,7 @@ In the 'Site Manager' dialog, click 'New site'
 
 In the 'New Site' dialog, create a name for the site, e.g. `bianca-sens123456`.
 
-## 6. Configure site 
+## 6. Configure site
 
 In the 'New Site' dialog, use all standards, except:
 

docs/cluster_guides/bianca_file_transfer_using_gui.md

@@ -31,7 +31,7 @@ one needs [to be inside of SUNET](../getting_started/get_inside_sunet.md).
 
     See the 'get inside the university networks' page [here](../getting_started/get_inside_sunet.md)
 
-When a tool is setup, one can only transfer files 
+When a tool is setup, one can only transfer files
 between you local computer and [your Bianca `wharf` folder](wharf.md).
 
 ## Bianca's constraints

docs/cluster_guides/lftp_with_bianca.md

@@ -3,9 +3,9 @@
 `lftp` is a command-line program
 to [transfer files to/from Bianca](transfer_bianca.md).
 
-With the command line SFTP client `lftp`, 
-you need to "set net:connection_limit 1". 
-`lftp` may also defer the actual connection 
+With the command line SFTP client `lftp`,
+you need to "set net:connection_limit 1".
+`lftp` may also defer the actual connection
 until it's really required unless you end your connect URL with a path.
 
 [When inside of SUNET](../getting_started/get_inside_sunet.md)
@@ -15,7 +15,7 @@ until it's really required unless you end your connect URL with a path.
 lftp sftp://[user_name]-[project_id]@bianca-sftp.uppmax.uu.se/[user_name]-[project_id]/
 ```
 
-where 
+where
 
  * `[project_id]` is the ID of your [NAISS project](../getting_started/project.md)
  * `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md)

docs/cluster_guides/project_management.md

@@ -11,13 +11,13 @@
 
 ???- question "What is this 'glob' folder in my home folder?"
 
-    - The glob directory found in your home has been deprecated since early 2017. 
-    - It is now a normal directory and shared your default 32GByte sized home. 
+    - The glob directory found in your home has been deprecated since early 2017.
+    - It is now a normal directory and shared your default 32GByte sized home.
     - The glob directory remains to not interfere with scripts who might reference ~/glob in the source code.
 
-    - Historically, the glob directory was the main storage area for storage of user data. 
-        - It was shared by all nodes. 
-        - The directory was used for files needed by all job instances and could house files exceeding the quota of the home directory. 
+    - Historically, the glob directory was the main storage area for storage of user data.
+        - It was shared by all nodes.
+        - The directory was used for files needed by all job instances and could house files exceeding the quota of the home directory.
         - Job input and output files was (and can still be) stored here.
 
 ## Members

docs/cluster_guides/rsync_on_bianca.md

@@ -1,6 +1,6 @@
 # `rsync` on Bianca
 
-[`rsync`](../software/rsync.md) is a command-line tool 
+[`rsync`](../software/rsync.md) is a command-line tool
 for [file transfer](../cluster_guides/file_transfer.md).
 
 This page describes how to use [`rsync`](../software/rsync.md) on [Bianca](bianca.md).
@@ -12,18 +12,18 @@ One cannot `rsync` directly to `wharf`.
     One cannot `rsync` directly to `wharf`.
 
     However, this is how it looks like:
-    
+
 
 	```
 	richel@richel-N141CU:~$ rsync my_local_file.txt [email protected]:/richel-sens2016001
 
 	Hi!
 
-	You are connected to the bianca wharf (sftp service) at 
+	You are connected to the bianca wharf (sftp service) at
 	bianca-sftp.uppmax.uu.se.
 
 	Note that we only support SFTP, which is not exactly the
-	same as SSH (rsync and scp will not work). 
+	same as SSH (rsync and scp will not work).
 
 	Please see our homepage and the Bianca User Guide
 	for more information:
@@ -36,7 +36,7 @@ One cannot `rsync` directly to `wharf`.
 	Best regards,
 	UPPMAX
 
-	[email protected]'s password: 
+	[email protected]'s password:
 	protocol version mismatch -- is your shell clean?
 	(see the rsync manpage for an explanation)
 	rsync error: protocol incompatibility (code 2) at compat.c(622) [sender=3.2.7]

docs/cluster_guides/running_jobs/storage_compression.md

@@ -7,16 +7,16 @@
 ???- question "How does automatic backup of project areas work at UPPMAX?"
 
     [Backup](../backup.md)
-    
+
 ???- question "What is this 'glob' folder in my home folder?"
 
-    - The glob directory found in your home has been deprecated since early 2017. 
-    - It is now a normal directory and shared your default 32GByte sized home. 
+    - The glob directory found in your home has been deprecated since early 2017.
+    - It is now a normal directory and shared your default 32GByte sized home.
     - The glob directory remains to not interfere with scripts who might reference ~/glob in the source code.
 
-    - Historically, the glob directory was the main storage area for storage of user data. 
-        - It was shared by all nodes. 
-        - The directory was used for files needed by all job instances and could house files exceeding the quota of the home directory. 
+    - Historically, the glob directory was the main storage area for storage of user data.
+        - It was shared by all nodes.
+        - The directory was used for files needed by all job instances and could house files exceeding the quota of the home directory.
         - Job input and output files was (and can still be) stored here.
 
     - You might also be interested in our [disk storage guide](../storage/disk_storage_guide.md).

docs/cluster_guides/sftp_with_bianca.md

@@ -16,7 +16,7 @@ to [transfer files to/from Bianca](transfer_bianca.md).
 sftp [user_name]-[project_id]@bianca-sftp.uppmax.uu.se:/[user_name]-[project_id]
 ```
 
-where 
+where
 
  * `[project_id]` is the ID of your [NAISS project](../getting_started/project.md)
  * `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md)
@@ -30,12 +30,12 @@ sftp [email protected]:/sven-sens2016001
 `sftp` will ask for a password:
 
 ```
-[email protected]'s password: 
+[email protected]'s password:
 ```
 
 The password is your normal UPPMAX password directly followed by
 the six digits from the [the `UPPMAX` 2-factor authentication](https://www.uu.se/en/centre/uppmax/get-started/2-factor).
-For example, if your password is `VerySecret` and the second factor code is `123456` 
+For example, if your password is `VerySecret` and the second factor code is `123456`
 you would type `VerySecret123456` as the password in this step.
 
 After typing in the password and 2FA one sees a welcome message
@@ -48,11 +48,11 @@ and the `sftp` prompt.
     ```
     Hi!
 
-	You are connected to the bianca wharf (sftp service) at 
+	You are connected to the bianca wharf (sftp service) at
 	bianca-sftp.uppmax.uu.se.
 
 	Note that we only support SFTP, which is not exactly the
-	same as SSH (rsync and scp will not work). 
+	same as SSH (rsync and scp will not work).
 
 	Please see our homepage and the Bianca User Guide
 	for more information:
@@ -65,9 +65,9 @@ and the `sftp` prompt.
 	Best regards,
 	UPPMAX
 
-	[email protected]'s password: 
+	[email protected]'s password:
 	Connected to bianca-sftp.uppmax.uu.se.
-	sftp> 
+	sftp>
 	```
 
 ???- question "How do I get rid of the welcome message?"
@@ -81,7 +81,7 @@ and the `sftp` prompt.
 The last line, `sftp> ` is the `sftp` prompt.
 
 
-Once connected you will have to type the `sftp` commands to upload/download files. 
+Once connected you will have to type the `sftp` commands to upload/download files.
 See [the UPPMAX page on `sftp`](../software/sftp.md) how to do so.
 
 With `sftp` you only have access to [your wharf folder](wharf.md).

docs/cluster_guides/software_on_transit.md

@@ -1,15 +1,15 @@
 # Software on Transit
 
-[Transit](../cluster_guides/transit.md) 
+[Transit](../cluster_guides/transit.md)
 is an UPPMAX service that can be used to securely transfer files.
 
 This page describes the software on [Transit](../cluster_guides/transit.md).
 
 After [logging in to Transit](../cluster_guides/login_transit.md),
-you cannot make lasting changes to anything, 
-except for mounted [wharf](../cluster_guides/wharf.md) directories. 
-However, anything you have added to your [Rackham](../cluster_guides/rackham.md) home directory 
-is available on [Transit](../cluster_guides/transit.md). 
+you cannot make lasting changes to anything,
+except for mounted [wharf](../cluster_guides/wharf.md) directories.
+However, anything you have added to your [Rackham](../cluster_guides/rackham.md) home directory
+is available on [Transit](../cluster_guides/transit.md).
 
 In addition, some modules are available.
 
@@ -24,18 +24,18 @@ In addition, some modules are available.
     ```
   ![dds-cli](../img/dds-cli.png)
 
-To download data from TCGA, 
-[log in to Rackham](../getting_started/login_rackham.md) 
-and install the GDC client to your home directory. 
-Then [log in to Transit](../cluster_guides/login_transit.md), 
-mount the [wharf](../cluster_guides/wharf.md), 
+To download data from TCGA,
+[log in to Rackham](../getting_started/login_rackham.md)
+and install the GDC client to your home directory.
+Then [log in to Transit](../cluster_guides/login_transit.md),
+mount the [wharf](../cluster_guides/wharf.md),
 and run `./gdc-client`.
 
 !!! warning "2FA on transit"
 
-    If you connect from abroad and 
-    you are asked for the **2FA** (_two factor authentication_), 
-    there is a grace period (_about 5 minutes_) in which you can 
-    `ssh`/`scp`/`rsync`/`sftp` to **transit** without the need for **2FA**. 
-    This allows you to use these and other tools 
+    If you connect from abroad and
+    you are asked for the **2FA** (_two factor authentication_),
+    there is a grace period (_about 5 minutes_) in which you can
+    `ssh`/`scp`/`rsync`/`sftp` to **transit** without the need for **2FA**.
+    This allows you to use these and other tools
     that might experience problems with the **2FA**.

docs/cluster_guides/storage/compress_guide.md

@@ -10,7 +10,7 @@ We have several compression programs installed and you are free to chose whichev
 gzip also has a parallel version (pigz) that will let the program use multiple cores, making it much faster. If you want to run multithreaded you should make a reservation in the queue system, as the login nodes will throttle your programs if they use too much resources.
 
 ```
-# compress a file 
+# compress a file
 $ gzip file.txt            # single threaded
 $ pigz -p 4 file.txt       # using 4 threads
 # decompress a file
@@ -23,7 +23,7 @@ $ unpigz -p 4 file.txt     # using 4 threads (4 is max)
 bzip2 also has a parallel version (pbzip2) that will let the program use multiple cores, making it much faster. If you want to run multithreaded you should make a reservation in the queue system, as the login nodes will throttle your programs if they use too much resources.
 
 ```
-# compress a file 
+# compress a file
 $ bzip2 file.txt            # single threaded
 $ pbzip2 -p4 file.txt       # using 4 threads
 # decompress a file
@@ -36,7 +36,7 @@ $ pbunzip2 -p4 file.txt.gz  # using 4 threads
 zstd has built in support for using multiple threads when compressing data only, making it much faster. If you want to run multithreaded you should make a reservation in the queue system, as the login nodes will throttle your programs if they use too much resources.
 
 ```
-# compress a file 
+# compress a file
 $ zstd --rm file.txt        # single threaded
 $ zstd --rm -T4 file.txt    # using 4 threads
 # decompress a file, only single threaded
@@ -48,7 +48,7 @@ The commands above work on a single file at a time, and if you have 1000s of fil
 
 ```
 # to compress a folder (folder/)
-# and all files/folder inside it, 
+# and all files/folder inside it,
 # creating a archive file named files.tar.gz
 $ tar -czvf files.tar.gz folder/
 # to decompress the archive later
@@ -76,7 +76,7 @@ There are some compression algorithms that have become standard practice to use
 ### fastq files
 
 ```
-# compress sample.fq 
+# compress sample.fq
 $ gzip sample.fq        # single threaded
 $ pigz -p 4 sample.fq   # using 4 threads
 ```
@@ -103,7 +103,7 @@ $ module load bioinfo-tools htslib
 # compress sample.vcf / sample.g.vcf
 $ bgzip sample.vcf         # single threaded
 $ bgzip -@ 4 sample.vcf    # using 4 threads
-# index sample.vcf.gz / sample.g.vcf.gz 
+# index sample.vcf.gz / sample.g.vcf.gz
 $ tabix sample.vcf.gz
 ```
 

docs/cluster_guides/transfer_bianca.md

@@ -16,7 +16,7 @@ flowchart LR
   end
 ```
 
-[File transfer](file_transfer.md) is the process of getting files 
+[File transfer](file_transfer.md) is the process of getting files
 from one place to the other. This page shows how to do [file transfer](file_transfer.md) to/from
 the [Bianca](bianca.md) UPPMAX cluster.
 
@@ -61,8 +61,8 @@ See [using `lftp` with Bianca](lftp_with_bianca.md).
 
 ## Transit server
 
-To facilitate secure data transfers to, from, 
-and within the system for computing on sensitive data a special service is available 
+To facilitate secure data transfers to, from,
+and within the system for computing on sensitive data a special service is available
 via SSH at `transit.uppmax.uu.se`.
 
 ![A user that is logged in to Transit](./img/logged_in_transit.png)
@@ -103,10 +103,10 @@ rsync -avh [email protected]:path/my_files ~/sens2023531/
 
 ### Moving data between projects
 
-- You can use transit to transfer data between projects 
-  by mounting the wharfs for the different projects 
+- You can use transit to transfer data between projects
+  by mounting the wharfs for the different projects
   and transferring data with `rsync`.
-- Note that you may of course only do this if this is allowed 
+- Note that you may of course only do this if this is allowed
   (agreements, permissions, etc.)
 
 ## Mounting `wharf` on your local computer

docs/cluster_guides/transit.md

@@ -1,6 +1,6 @@
 # Transit
 
-[Transit](../cluster_guides/transit.md) 
+[Transit](../cluster_guides/transit.md)
 is an UPPMAX service that can be used to securely transfer files.
 
 ???- question "Is Transit a file server?"