Moving default resources to OpenOmics shared group area and adding en…

…hancements for increased portability

config/cluster.json

@@ -2,7 +2,6 @@
     "__default__": {
         "threads": "4",
         "mem": "8g",
-        "partition": "norm",
         "time": "0-04:00:00",
         "gres": "lscratch:64"
     },

config/containers.json

@@ -1,13 +1,6 @@
 {
     "images": {
-        "cutadapt": "/data/NCBR/dev/SIFs/ccbr_cutadapt_1.18_v032219.sif",
-        "fastq_screen": "/data/NCBR/dev/SIFs/ccbr_fastq_screen_0.13.0_v2.0.sif",
-        "fastqc": "/data/NCBR/dev/SIFs/ccbr_fastqc_0.11.9_v1.1.sif",
-        "fastqvalidator": "/data/NCBR/dev/SIFs/ccbr_fastqvalidator_v0.1.0.sif",
-        "kraken": "/data/NCBR/dev/SIFs/ccbr_kraken_v2.1.1_v0.0.1.sif",
-        "metaquast": "/data/NCBR/dev/SIFs/quast_5.0.2--py27pl526ha92aebf_0.sif",
-        "metavirs": "docker://skchronicles/metavirs:v0.1.0",
-        "multiqc": "/data/NCBR/dev/SIFs/ccbr_multiqc_1.9_v0.0.1.sif",
-        "python": "/data/NCBR/dev/SIFs/ccbr_python_v0.0.1.sif"
+        "fastqvalidator": "docker://nciccbr/ccbr_fastqvalidator:v0.1.0",
+        "metavirs": "docker://skchronicles/metavirs:v0.1.0"
     }
-}
+}

config/genome.json

@@ -1,12 +1,12 @@
 {
     "references": {
         "adapters": "resources/TruSeq_and_nextera_adapters.fa",
-        "host_bowtie2_index": "/data/NCBR/references/metavirs/bowtie2/",
-        "kraken2_viral_db": "/data/NCBR/references/metavirs/kraken2/viral/",
-        "kronatools": "/data/NCBR/references/metavirs/kronatax_0921/",
-        "CAT_db": "/data/NCBR/references/metavirs/CAT_prepare_20210107/2021-01-07_CAT_database",
-        "CAT_taxonomy": "/data/NCBR/references/metavirs/CAT_prepare_20210107/2021-01-07_taxonomy",
-        "CAT_diamond": "/data/NCBR/references/metavirs/CAT_prepare_20210107/Diamond_2.0.6/diamond",
-        "ncbi_viral_fasta": "/data/NCBR/references/metavirs/ncbi/viral_oneline.fa"
+        "host_bowtie2_index": "/data/OpenOmics/references/metavirs/bowtie2/",
+        "kraken2_viral_db": "/data/OpenOmics/references/metavirs/kraken2/viral/",
+        "kronatools": "/data/OpenOmics/references/metavirs/kronatax_0921/",
+        "CAT_db": "/data/OpenOmics/references/metavirs/CAT_prepare_20210107/2021-01-07_CAT_database",
+        "CAT_taxonomy": "/data/OpenOmics/references/metavirs/CAT_prepare_20210107/2021-01-07_taxonomy",
+        "CAT_diamond": "/data/OpenOmics/references/metavirs/CAT_prepare_20210107/Diamond_2.0.6/diamond",
+        "ncbi_viral_fasta": "/data/OpenOmics/references/metavirs/ncbi/viral_oneline.fa"
     }
 }

src/run.py

@@ -715,7 +715,7 @@ def runner(mode, outdir, alt_cache, logger, additional_bind_paths = None,
         # Look into later: it maybe worth 
         # replacing Popen subprocess with a direct
         # snakemake API call: https://snakemake.readthedocs.io/en/stable/api_reference/snakemake.html
-        # CLUSTER_OPTS="'sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} \
+        # CLUSTER_OPTS="'sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} \
         #   -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURMDIR/slurm-%j_{params.rname}.out \
         #   -o $SLURMDIR/slurm-%j_{params.rname}.out'"
         # sbatch --parsable -J "$2" --gres=lscratch:500 --time=5-00:00:00 --mail-type=BEGIN,END,FAIL \

src/run.sh

@@ -192,7 +192,7 @@ function submit(){
           # --keep-remote --restart-times 3 -j 50 --use-singularity 
           # --singularity-args -B {}.format({bindpaths}) --local-cores 24
           SLURM_DIR="$3/logfiles/slurmfiles"
-          CLUSTER_OPTS="sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
+          CLUSTER_OPTS="sbatch --gres {cluster.gres} --cpus-per-task {cluster.threads} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
           # Check if NOT running on Biowulf
           # Assumes other clusters do NOT 
           # have GRES for local node disk,
@@ -207,7 +207,7 @@ function submit(){
           # SLURM is not configured to use 
           # GRES, remove prefix single quote
           if [[ ${6#\'} != /lscratch* ]]; then
-            CLUSTER_OPTS="sbatch --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
+            CLUSTER_OPTS="sbatch --cpus-per-task {cluster.threads} -t {cluster.time} --mem {cluster.mem} --job-name={params.rname} -e $SLURM_DIR/slurm-%j_{params.rname}.out -o $SLURM_DIR/slurm-%j_{params.rname}.out"
           fi
           # Create sbacth script to build index
     cat << EOF > kickoff.sh