adjusted directory paths

Author: LucvZon

posts/IMAM-05-annotation.qmd

@@ -26,7 +26,7 @@ diamond blastx \
 -   `{db}` is the protein database to be searched against.
 -   `{output}` is a .tsv file containing the annotation results.
 
-Multiple different databases can be found in: `\\cifs.research.erasmusmc.nl\viro0002\workgroups_projects\Bioinformatics\DB`
+Multiple different databases can be found in: `/mnt/viro0002-data/workgroups_projects/Bioinformatics/DB`
 
 ## 4.2 Split annotation files {.unnumbered}
 
@@ -63,12 +63,12 @@ rmdir tmp_split
 
 ## 4.3 Parsing diamond output {.unnumbered}
 
-Now we will process the DIAMOND output files with a custom Python script called **post_process_diamond.py**. This script will further enrich taxonomic information for each contig based on the DIAMOND alignment results. If a contig has multiple matches in the database, it will select the best hit based on a combined score of bitscore and length. Lastly, it separates the contigs into two lists: those that were successfully annotated and unannotated.
+Now we will process the DIAMOND output files with a custom Python script called **post_process_diamond_v1.0.py**. This script will further enrich taxonomic information for each contig based on the DIAMOND alignment results. If a contig has multiple matches in the database, it will select the best hit based on a combined score of bitscore and length. Lastly, it separates the contigs into two lists: those that were successfully annotated and unannotated.
 
 This python script utilizes the [biopython library](https://biopython.org/){target="_blank"}.
 
 ``` bash
-python /mnt/viro0002/workgroups_projects/Bioinformatics/scripts/post_process_diamond.py \
+python /mnt/viro0002-data/workgroups_projects/Bioinformatics/scripts/post_process_diamond_v1.0.py \
 -i {input.annotation} \
 -c {input.contigs} \
 -o {output.annotated} \

posts/IMAM-07-illumina_hpc.qmd

@@ -45,7 +45,7 @@ Now prepare your project directory with prepare_project.py as follows:
 
 ``` bash
 singularity exec \
-  --bind /mnt/viro0002:/mnt/viro0002 \
+  --bind /mnt/viro0002-data:/mnt/viro0002-data \
   --bind $HOME:$HOME \
   --bind $PWD:$PWD \
   imam_workflow.sif \
@@ -62,7 +62,7 @@ singularity exec \
 
 The `--bind` arguments are needed to explicitly tell Singularity to mount the necessary host directories into the container. The part before the colon is the path on the host machine that you want to make available. The path after the colon is the path inside the container where the host directory should be mounted. 
 
-As a default, Singularity often automatically binds your home directory (`$HOME`) and the current directory (`$PWD`). We also explicitly bind `/mnt/viro0002` in this example. If your input files (reads, reference, databases) or output project directory reside outside these locations, you MUST add specific `--bind /host/path:/container/path` options for those locations, otherwise the container won't be able to find them.
+As a default, Singularity often automatically binds your home directory (`$HOME`) and the current directory (`$PWD`). We also explicitly bind `/mnt/viro0002-data` in this example. If your input files (reads, reference, databases) or output project directory reside outside these locations, you MUST add specific `--bind /host/path:/container/path` options for those locations, otherwise the container won't be able to find them.
 
 ::: callout-note
 When prepare_project.py prompts for the Reference and DB paths, you must enter the absolute host paths, and these paths must be accessible via one of the bind mounts.
@@ -88,7 +88,7 @@ Run inside of your project directory:
 
 ``` bash
 singularity exec \
-  --bind /mnt/viro0002:/mnt/viro0002 \
+  --bind /mnt/viro0002-data:/mnt/viro0002-data \
   --bind $HOME:$HOME \
   --bind $PWD:$PWD \
   imam_workflow.sif \