update READMEs

README.md

 # HTCondor Examples
 
-This is a collection of working examples to demonstrate best practices and to
-speed bootstrapping of new projects on Juseless.
+A collection of working examples to speed bootstrapping of new projects on
+Juseless and demonstrate best practices.
 
 If you see something that is missing or should be improved, please contribute!
 
 | name                         | description                                   |
 | ----                         | -----------                                   |
-| [fMRIPrep](fmriprep/)        |                                               |
-| [matlab](matlab/)            |                                               |
-| [ncal](ncal/)                |                                               |
-| [python](python/)            |                                               |
-
+| [fMRIPrep](fmriprep/)        | A full-featured template that uses a script to generate the submit file. |
+| [matlab](matlab/)            | A very simple submit file that passes an argument to a Matlab script. |
+| [ncal](ncal/)                | The [calendar printing example](https://docs.inm7.de/tools/htcondor/#generating-a-submit) used in the docs. A script is used to generate the submit file. |
+| [python](python/)            | A very simple submit file that passes an argument to a Python script. |

fmriprep/README.md

 # fMRIPrep
 
-This template serves only as an example. It will need to be adapted in order to
-run for your project. Most importantly the
+This template uses a script (`gen_submit.sh`) to generate the submit file.
+
+This template will need to be adapted in order to run for your project. Most
+importantly the
 
 1) `bids_dir`
 2) `output_dir`
 3) [command-line arguments](https://fmriprep.readthedocs.io/en/stable/usage.html#command-line-arguments)
-   to control which workflows are run
+   to control which workflows are run. If you're unsure about which options to
+   use, talk with your group leader.
+4) subject for-loop
 
 ## Prerequisites
 * a BIDS dataset
 
 ## Things to Note
-* a library of fMRIPrep images are stored on Juseless in `/data/project/singularity`.
+* a collection of fMRIPrep images are stored in `/data/project/singularity` on
+  Juseless.
 * **CPU:**: 1 CPU was chosen as (with the option used in this example) there was
   no appreciable speed difference between 1 CPU and multi-CPU jobs.
 * **RAM:** 8GB is [recommended by upstream](https://brainscan.uwo.ca/research/cores/computational_core/img/Nov26-Fmriprep.pdf)
@@ -26,7 +31,11 @@ Adjust the variables in the script, most especially the `BIDS_DIR`,
 `OUTPUT_DIR`, and `FMRIPREP`. Also adjust the subjects for-loop to meet your
 needs.
 
-When you've made your changes, run it like so:
+Once you've made your changes, verify that it's working:
+```
+./gen_submit.sh
+```
+If the output looks correct, then submit the jobs like so:
 ```
 ./gen_submit.sh | condor_submit
 ```

matlab/README.md

 # Matlab
-
 The `matlab.submit` file submits one job that calls `analyze_subject.m` ---
 which simply prints out the subject ID that is passed to it.
 
@@ -29,7 +28,6 @@ should read the INM-7 Docs section on
 
 To restrict your jobs to two machines, add the following to your submit file
 (adjust the machine names to your needs):
-
 ```
 requirements = Machine == "cpu7.htc.inm7.de" || Machine == "cpu8.htc.inm7.de"
 ```

ncal/README.md

@@ -4,8 +4,9 @@ The `ncal_submit_gen.sh` generates a submit file with a series of jobs. Each job
 calls `ncal` --- which prints the calendar for that year.
 
 To run:
-
-```./ncal_submit_gen.sh | condor_submit```
+```
+./ncal_submit_gen.sh | condor_submit
+```
 
 ## Prerequisites
 This example assumes that it is located in `~/htcondor-templates/ncal`. If you

python/README.md

 # Python
-
 The `python.submit` file submits one job that calls `analyze_subject.py` ---
 which simply prints out the subject ID that is passed to it.