Feedback after reading tutorials

docs/tutorials/tutorial0.md

@@ -6,7 +6,7 @@ Janis was designed with a few points in mind:
 
 - Workflows should be easy to build,
 - Workflows and tools must be easily shared (portable),
-- Workflows should be able to execute on HPCs and cloud environments.
+- Workflows should be able to execute on HPCs and cloud environments,
 - Workflows should be reproducible and re-runnable.
 
 Janis uses an *abstracted execution environment*, which removes the shared file system in favour of you specifiying all the files you need up front and passing them around as a File object. This allows the same workflow to be executable on your local machine, HPCs and cloud, and we let the `execution engine` handle moving our files. This also means that we can use file systems like ``S3``, ``GCS``, ``FTP`` and more without any changes to our workflow.
@@ -63,7 +63,7 @@ We'll install Janis in a virtual environment as it preserves versioning of Janis
 pip install cwltool
 ```
 
-Test that CWLTool has installed correctly with:
+Test that CWLTool has been installed correctly with:
 
 ```bash
 cwltool --version
@@ -80,6 +80,13 @@ mkdir ~/janis
 cd ~/janis
 ```
 
+Let's also create a directory to store the files for the tutorials.
+
+```bash
+mkdir janis-tutorials
+cd janis-tutorials
+```
+
 You can test run an example workflow with Janis and CWLTool with the following command:
 
 ```bash
@@ -112,7 +119,7 @@ janis watch d909df
 # Name:       hello
 # Engine:     cwltool
 # 
-# Task Dir:   $HOME/janis/tutorial0
+# Task Dir:   $HOME/janis/janis-tutorials/tutorial0
 # Exec Dir:   None
 # 
 # Status:     Completed
@@ -125,13 +132,13 @@ janis watch d909df
 #     [✓] hello (1s)       
 # 
 # Outputs:
-#     - out: $HOME/janis/tutorial0/out
+#     - out: $HOME/janis/janis-tutorials/tutorial0/out
 ```
 
 There is a single output `out` from the workflow, cat-ing this result we get:
 
 ```bash
-cat $HOME/janis/tutorial0/out
+cat $HOME/janis/janis-tutorials/tutorial0/out
 # Hello, World
 ```
 
@@ -152,7 +159,7 @@ janis run --engine cwltool -o tutorial0-override hello --inp "Hello, $(whoami)"
 
 ### Running Janis in the background
 
-You may want to run Janis in the background as it's own process. You could do this with `nohup [command] &`, however we can also run Janis with the `--background` flag and capture the workflow ID to watch, eg:
+You may want to run Janis in the background as its own process. You could do this with `nohup [command] &`, however we can also run Janis with the `--background` flag and capture the workflow ID to watch, eg:
 
 ```bash
 wid=$(janis run \
@@ -165,7 +172,7 @@ janis watch $wid
 
 ## Summary
 
-- Setup a virtualenv
+- Set up a virtualenv
 - Installed Janis and CWLTool
 - Ran a small workflow with custom inputs
 

docs/tutorials/tutorial1.md

@@ -1,5 +1,7 @@
 # Tutorial 1 - Building a Workflow
 
+> This tutorial uses directories created in [Tutorial 0](https://janis.readthedocs.io/en/latest/tutorials/tutorial0.html).
+
 In this stage, we're going to build a simple workflow to align short reads of DNA.
 
 1. Start with a pair of compressed `FASTQ` files,
@@ -15,16 +17,16 @@ These tools already exist within the Janis Tool Registry, you can see their docu
 
 ## Preparation
 
-To prepare for this tutorial, we're going to create a folder and download some data:
+To prepare for this tutorial, we're going to need to download some data first:
 
 ```bash
-mkdir janis-tutorials && cd janis-tutorials
+cd ~/janis/janis-tutorials
 
 # If WGET is installed
-wget -q -O- "https://github.com/PMCC-BioinformaticsCore/janis-workshops/raw/master/janis-data.tar" | tar -xz
+wget -q -O- "https://github.com/PMCC-BioinformaticsCore/janis-workshops/raw/master/janis-data.tar" | tar -x
 
 # If CURL is installed
-curl -Ls "https://github.com/PMCC-BioinformaticsCore/janis-workshops/raw/master/janis-data.tar" | tar -xz
+curl -Ls "https://github.com/PMCC-BioinformaticsCore/janis-workshops/raw/master/janis-data.tar" | tar -x
 ```
 
 
@@ -60,7 +62,7 @@ from janis_bioinformatics.data_types import FastqGzPairedEnd, FastaWithDict
 
 ### Tools
 
-We've discussed the tools we're going to use. The documentation for each tool has a row in the tbale caled "Python" that gives you the import statement. This is how we'll import how tools:
+We've discussed the tools we're going to use. The documentation for each tool has a row in the table caled "Python" that gives you the import statement. This is how we'll import these tools:
 
 
 ```python
@@ -129,7 +131,7 @@ Workflow.step(
 )
 ```
 
-We provide a identifier for the step (unique amongst the other nodes in the workflow), and intialise our tool, passing our inputs of the step as parameters.
+We provide an identifier for the step (unique amongst the other nodes in the workflow), and intialise our tool, passing our inputs of the step as parameters.
 
 We can refer to an input (or previous result) using the dot notation. For example, to refer to the `fastq` input, we can use `w.fastq`.
 
@@ -212,7 +214,7 @@ w.output("out", source=w.sortsam.out)
 
 ## Workflow + Translation
 
-Hopefully you have a workflow that looks like the following!
+Hopefully now you have a workflow that looks like the following!
 
 ```python
 from janis_core import WorkflowBuilder, String
@@ -272,33 +274,30 @@ janis translate tools/alignment.py wdl
 We'll run the workflow against the current directory.
 
 ```bash
-janis run -o . --engine cwltool \
+janis run -o tutorial1 --engine cwltool \
     tools/alignment.py \
     --fastq data/BRCA1_R*.fastq.gz \
     --reference reference/hg38-brca1.fasta \
     --sample_name NA12878 \
     --read_group "@RG\tID:NA12878\tSM:NA12878\tLB:NA12878\tPL:ILLUMINA"
 ```
 
-After the workflow has run, you'll see the outputs in the current directory:
+After the workflow has run, you'll see the outputs in the tutorial1 directory:
 
 ```bash
-ls
+ls ~/janis/janis-tutorials/tutorial1
 
-# drwxr-xr-x  mfranklin  1677682026   160B  data
 # drwxr-xr-x  mfranklin  1677682026   256B  janis
 # -rw-r--r--  mfranklin  wheel        2.7M  out.bam
 # -rw-r--r--  mfranklin  wheel        296B  out.bam.bai
-# drwxr-xr-x  mfranklin  1677682026   320B  reference
-# drwxr-xr-x  mfranklin  1677682026   128B  tools
 ```
 
 ### OPTIONAL: Run with Cromwell
 
 If you have `java` installed, Janis can run the workflow in the Crowmell execution engine by using the `--engine cromwell` parameter:
 
 ```bash
-janis run -o run-with-cromwell --engine cromwell \
+janis run -o tutorial1-run-with-cromwell --engine cromwell \
     tools/alignment.py \
     --fastq data/BRCA1_R*.fastq.gz \
     --reference reference/hg38-brca1.fasta \

docs/tutorials/tutorial2.md

@@ -73,7 +73,7 @@ ToolName = CommandToolBuilder(
 Let's start by creating a file with this template inside a second output directory:
 
 ```bash
-mkdir -p tools
+cd ~/janis/janis-tutorials
 vim tools/samtoolsflagstat.py
 ```
 
@@ -280,13 +280,13 @@ Jobs:
     [✓] samtoolsflagstat (N/A)       
 
 Outputs:
-    - stats: $HOME/janis-tutorials/tutorial2/stats.txt
+    - stats: $HOME/janis-tutorials/tutorial2/stats
 ```
 
 Janis (and CWLTool) said the tool executed correctly, let's check the output file: 
 
 ```bash
-cat tutorial2/stats.txt
+cat tutorial2/stats
 ```
 
 ```

docs/tutorials/tutorial3.md

@@ -16,7 +16,7 @@ This tutorial uses the workflow build in [Tutorial 1](https://janis.readthedocs.
 
 ## Output name
 
-Simply put, `output_name` is the dervied filename of the output without the extension. By default, this is the `tag` of the output.
+Simply put, `output_name` is the derived filename of the output without the extension. By default, this is the `tag` of the output.
 
 You can specify a new output name in 2 ways:
 
@@ -30,17 +30,17 @@ You should make the following considerations:
 - The input you select should be a string, or
 
 - If the output you're naming is an array, the input you select should either be:
-    - singular
+    - singular or
     - have the same number of elements in it.
 
-    Janis will either fall back to the first element if it's a list, or default to the output tag. This may cause outputs to override each other.
+Janis will either fall back to the first element if it's a list, or default to the output tag. This may cause outputs to override each other.
 
 
 ## Output folder
 
 Similar to the output name, the `output_folder` is folder, or group of nested folders into which your output will be written. By default, this field has no value and outputs are linked directly into the output directory.
 
-If the output_folder field is an array, a nested folder is created for each element in ascending order (eg: `["parent", "child", "child_of_child"]`).
+If the `output_folder` field is an array, a nested folder is created for each element in ascending order (eg: `["parent", "child", "child_of_child"]`).
 
 There are multiple ways to specify output directories:
 

setup.py

@@ -33,7 +33,6 @@
 modules = ["janis_assistant." + p for p in sorted(find_packages("./janis_assistant"))]
 
 
-fixed_unix_version = f"janis-pipelines.unix==" + JANIS_UNIX_VERSION
 setup(
     name="janis pipelines",
     version=__version__,