fix(docs): update docs for new snakemake version (#174)

* feat: updated install script

* Update FAQ and installation instructions

docs/faq.md

@@ -4,7 +4,9 @@
 
 ### Workflow defines configfile config_chip.yml but it is not present or accessible.
 
-This error occurs when the pipeline is run without a config file present in the working directory. Follow the [Pipeline Setup](pipeline.md#create-a-design-file) instructions to create a config file.
+This error occurs when the pipeline is run without a config file present in the working directory. Ensure that seqnado-config has been run before starting the pipeline and that you are in the new directory created by seqnado-config.
+
+Follow the [Pipeline Setup](pipeline.md#create-a-design-file) instructions to create a config file.
 
 
 ## Singularity configuration

docs/index.md

@@ -48,4 +48,8 @@ mv /path/to/design.csv /path/to/working-directory/made-by-seqnado-config/
 ```bash
 cd /path/to/working-directory/made-by-seqnado-config/
 seqnado [atac|chip|rna|snp] -c <number of cores> --preset [ss|ls] # ss = use cluster, ls = use local (not recommended)
+
+# An actual example would be:
+seqnado rna -c 8 --preset ss
+
 ```

docs/installation.md

@@ -51,7 +51,7 @@ bash <(curl -s https://raw.githubusercontent.com/alsmith151/SeqNado/master/insta
 Create a basic conda environment (with pip to install python packages) and activate it.
 
 ```bash
-mamba create -n seqnado pip
+mamba create -n seqnado pip "python>=3.12"
 conda activate seqnado
 ```
 
@@ -63,6 +63,23 @@ conda activate seqnado
 pip install seqnado
 ```
 
+#### Ensure that Environment variables are set
+
+Ensure that the environment variables are set correctly. This can be done by adding the following to your `.bashrc` or `.bash_profile`. Run this command to add the environment variables to your `.bashrc`:
+
+```bash
+echo export APPTAINER_BINDPATH="/ceph:/ceph, /project:/project, /databank:/databank" >> ~/.bashrc
+```
+
+Reload the `.bashrc` file:
+
+```bash
+source ~/.bashrc
+```
+
+Alternatively, start a new terminal session.
+
+
 #### Install from GitHub directly
 
 To install the latest version of the pipeline from GitHub (master branch), use the following command:

docs/pipeline.md

@@ -66,9 +66,9 @@ The configuration file can be edited manually if required e.g. using `nano` or t
 !!! Warning
     If you edit the configuration file manually, you must ensure that it is valid YAML syntax (ensure that you do not delete any colons, commas, or change the indentation). You can check that the file is valid using the following command:
 
-```bash
-nano config_chip.yml # Note to exit nano press ctrl+x and then "y" followed by "enter" to save
-```
+  ```bash
+  nano config_chip.yml # Note to exit nano press ctrl+x and then "y" followed by "enter" to save
+  ```
 
 ### Create a design file (optional)
 
@@ -102,26 +102,34 @@ If the fastq files are named in a way that seqnado can infer the sample names, t
 
 If the fastq files are not named in a way that seqnado can infer the sample names, then a design file can be generated using the `seqnado-design` command. You'll need to enter the working directory and generate a design file:
 
+
 ```bash
 cd 2024-01-13_test/
 seqnado-design chip /path/to/fastq/files/* # Note that you can use tab completion to complete the path to the fastq files
 ```
 
 This will generate a design file called `design.csv` in the working directory.
 
+!!! Warning
+  You need to specify the fastq files in the command line to use for the design generation e.g. in the current working directory:
+
+    ```bash 
+    seqnado-design chip *.fastq.gz
+    ```
+
 
 #### ATAC|RNA-seq design file
 
 An ATAC-seq or RNA-seq design file should look something like this:
 
 ```bash
-,r1,r2
+sample,r1,r2
 rna,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna_2.fastq.gz,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna_1.fastq.gz
 ```
 
 !!! Note
     The design file is a CSV file with the following columns:
-      * The first column is the sample name
+      * `sample` - The sample name. Altering this will change the name of the output files so can be useful for renaming samples.
       * `r1` - The path to the read 1 fastq file
       * `r2` - The path to the read 2 fastq file
 
@@ -131,13 +139,13 @@ rna,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna_2.fastq.gz,/tmp
 A ChIP assay design file should look something like this:
 
 ```bash
-,ip_r1,ip_r2,control_r1,control_r2,ip,control
+sample,ip_r1,ip_r2,control_r1,control_r2,ip,control
 CTCF,CTCF_CTCF_2.fastq.gz,CTCF_CTCF_1.fastq.gz,CTCF_input_2.fastq.gz,CTCF_input_1.fastq.gz,CTCF,input
 ```
 
 !!! Note
     The design file is a CSV file with the following columns:
-      * The first column is the sample name
+      * `sample` - The sample name. Altering this will change the name of the output files so can be useful for renaming samples.
       * `ip_r1` - The path to the IP read 1 fastq file
       * `ip_r2` - The path to the IP read 2 fastq file
       * `control_r1` - The path to the control read 1 fastq file
@@ -151,14 +159,14 @@ CTCF,CTCF_CTCF_2.fastq.gz,CTCF_CTCF_1.fastq.gz,CTCF_input_2.fastq.gz,CTCF_input_
 An RNA-seq design file should look something like this:
 
 ```bash
-,r1,r2
+sample,r1,r2
 rna,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna_2.fastq.gz,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna_1.fastq.gz
 ```
 
 If you want to run DeSeq2, then you will need to add an additional column to the design file to indicate which samples are in the control group:
 
 ```bash
-,r1,r2,deseq2
+sample,r1,r2,deseq2
 rna1,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna1_2.fastq.gz,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna1_1.fastq.gz,control
 rna2,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna2_2.fastq.gz,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna2_1.fastq.gz,control
 rna3,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna3_2.fastq.gz,/tmp/pytest-of-asmith/pytest-7/data2/2024-01-13_rna_test/rna3_1.fastq.gz,control
@@ -203,11 +211,13 @@ tmux new -s NAME_OF_SESSION
 
 screen -S NAME_OF_SESSION
 
+# to detach from tmux session
+  ctrl+b d
+
 # to exit screen session
   ctrl+a d 
 ```
 
-
 ### Check you have activated the conda environment
 
 ```bash

install_seqnado.sh

@@ -10,20 +10,28 @@ if ! command -v mamba &> /dev/null; then
   export PATH="$HOME/mambaforge/bin:$PATH"
 fi
 
+
 # Create a new conda environment
 echo "Creating a new conda environment..."
-mamba create -n seqnado "python>3.10" pip -y
+mamba create -n seqnado_dev "python>=3.12" pip -y
 
 # Activate the conda environment
 echo "Activating the conda environment..."
-conda activate seqnado
+conda activate seqnado_dev
 
 # Install the seqnado package using pip
 echo "Installing seqnado..."
 pip install seqnado
 
 # Deactivate the conda environment
 echo "Deactivating the conda environment..."
-conda deactivate
+conda activate base
+
+# Set the environment variables for CCB
+if [[ $(hostname) =~ "imm-" ]]; then
+  echo export APPTAINER_BINDPATH="/ceph:/ceph, /project:/project, /databank:/databank" >> ~/.bashrc
+  export APPTAINER_BINDPATH="/ceph:/ceph, /project:/project, /databank:/databank"
+fi
+
 
 echo "Done!"