Replace abricate_exercise.md

exercises/abricate_exercise.md

@@ -14,11 +14,20 @@
 
         srun --pty -n 1 -c 2 --time=01:00:00 --mem=1G bash -l 
         module load singularityce
-        srun /shares/amr.imm.uzh/bioinfo/singularity/abricate_1.0.1--ha8f3691_1.sif abricate --list
+        srun /shares/amr.imm.uzh/bioinfo/singularity/quay.io-biocontainers-abricate-1.0.1--ha8f3691_1.img abricate --list
 
 -   This will generate the following output
 
-    DATABASE SEQUENCES DBTYPE DATE card 2631 nucl 2021-Mar-27 resfinder 3077 nucl 2021-Mar-27 megares 6635 nucl 2021-Mar-27 ncbi 5386 nucl 2021-Mar-27 argannot 2223 nucl 2021-Mar-27 plasmidfinder 460 nucl 2021-Mar-27 ecoh 597 nucl 2021-Mar-27 ecoli_vf 2701 nucl 2021-Mar-27 vfdb 2597 nucl 2021-Mar-27
+        DATABASE SEQUENCES DBTYPE DATE 
+        card 2631 nucl 2021-Mar-27 
+        resfinder 3077 nucl 2021-Mar-27 
+        megares 6635 nucl 2021-Mar-27 
+        ncbi 5386 nucl 2021-Mar-27 
+        argannot 2223 nucl 2021-Mar-27 
+        plasmidfinder 460 nucl 2021-Mar-27 
+        ecoh 597 nucl 2021-Mar-27 
+        ecoli_vf 2701 nucl 2021-Mar-27 
+        vfdb 2597 nucl 2021-Mar-27
 
 ### Screen your genomes for resistance genes and virulence factors
 
@@ -30,11 +39,11 @@
 
     Add the following parameters `--quiet --nopath --db [DATABASE]`
 
-    Run abricate twice, once on `ncbi` and once `vfdb`
+    Run abricate twice, once on `ncbi`, `card` and `vfdb`, respectively
 
     The Singularity image can be found at
 
-        /shares/amr.imm.uzh/bioinfo/singularity7quay.io-biocontainers-abricate-1.0.1--ha8f3691_1.img
+        /shares/amr.imm.uzh/bioinfo/singularity/quay.io-biocontainers-abricate-1.0.1--ha8f3691_1.img
 
     Use the following SLURM parameters:
 
@@ -47,5 +56,4 @@
         #SBATCH --output=abricate\_%A\_%a.out 
         #SBATCH --error=abricate\_%A\_%a.err
 
--   **Supplement:**
-    Screen for plasmids as well
+-   **Supplement:** Screen for plasmids as well