Merge pull request #167 from CCBR/iss-125

refactor: consolidate build_cluster.json into main cluster.json
CCBR · Nov 7, 2024 · 7cc0322 · 7cc0322
2 parents 06fd833 + eb1977f
commit 7cc0322
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Showing 8 changed files with 29 additions and 43 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,7 @@
 ## RENEE development version
 
+- Consolidate `build_cluster.json` into `cluster.json`. (#167, @kelly-sovacool)
+
 ## RENEE 2.6.1
 
 - New contributing guide available on GitHub and the documentation website. (#159, @kelly-sovacool)

diff --git a/resources/cluster.json → config/cluster.json b/resources/cluster.json → config/cluster.json
@@ -1,9 +1,9 @@
 {
     "__default__": {
-        "gres": "lscratch:256",
-        "mem": "48g",
+        "gres": "lscratch:128",
+        "mem": "8g",
         "partition": "norm",
-        "threads": "4",
+        "threads": "1",
         "time": "4:00:00",
         "name": "{rule}.{wildcards}",
         "output": "logfiles/slurmfiles/${{SLURM_JOBID}}.%j.{rule}.{wildcards}.out",
@@ -50,9 +50,13 @@
         "threads": "16",
         "time": "1-00:00:00"
     },
+    "qualimapinfo": {
+        "mem": "20g"
+    },
     "rsem": {
         "gres": "lscratch:500",
-        "threads": "16",
+        "mem": "48g",
+        "threads": "32",
         "time": "1-00:00:00"
     },
     "star1p": {
@@ -78,6 +82,18 @@
         "threads": "32",
         "time": "2-00:00:00"
     },
+    "star_rl": {
+        "mem": "48g",
+        "gres": "lscratch:128",
+        "threads": "32",
+        "time": "12:00:00"
+    },
+    "star_genome": {
+        "mem": "48g",
+        "gres": "lscratch:128",
+        "threads": "32",
+        "time": "12:00:00"
+    },
     "arriba": {
         "gres": "lscratch:256",
         "mem": "110g",

diff --git a/config/templates/project.json b/config/templates/project.json
@@ -6,7 +6,7 @@
         "MINSAMPLES": "0.5",
         "annotation": "",
         "binset": "standard-bin",
-        "cluster": "resources/cluster.json",
+        "cluster": "config/cluster.json",
         "contrasts": {
             "rcontrasts": ""
         },

diff --git a/resources/build_cluster.json b/resources/build_cluster.json
diff --git a/resources/builder b/resources/builder
@@ -211,7 +211,7 @@ function submit(){
             --output "$3"/logfiles/snakemake.log --error "$3"/logfiles/snakemake.log \
             snakemake --latency-wait 120 -s "$3"/workflow/rules/build.smk -d "$3" \
               --use-singularity --singularity-args "'-B $4'" --configfile="$3"/config/build.yml \
-              --printshellcmds --cluster-config "$3"/resources/build_cluster.json \
+              --printshellcmds --cluster-config "$3"/config/cluster.json \
               --cluster "${CLUSTER_OPTS}" \
               $triggeroptions \
               --keep-going --restart-times 3 -j 500 --rerun-incomplete --stats "$3"/logfiles/runtime_statistics.json \
@@ -221,7 +221,7 @@ function submit(){
             --output "$3"/logfiles/snakemake.log --error "$3"/logfiles/snakemake.log \
             snakemake --latency-wait 120 -s "$3"/workflow/rules/build.smk -d "$3" \
               --use-singularity --singularity-args "'-B $4'" --configfile="$3"/config/build.yml \
-              --printshellcmds --cluster-config "$3"/resources/build_cluster.json \
+              --printshellcmds --cluster-config "$3"/config/cluster.json \
               --cluster "${CLUSTER_OPTS}" \
               $triggeroptions \
               --keep-going --restart-times 3 -j 500 --rerun-incomplete --stats "$3"/logfiles/runtime_statistics.json \

diff --git a/resources/runner b/resources/runner
@@ -214,7 +214,7 @@ function submit(){
             --output "$3"/logfiles/snakemake.log --error "$3"/logfiles/snakemake.log \
             snakemake --latency-wait 120 -s "$3"/workflow/Snakefile -d "$3" \
               --use-singularity --singularity-args "'-B $4'" --configfile="$3"/config.json \
-              --printshellcmds --cluster-config "$3"/resources/cluster.json \
+              --printshellcmds --cluster-config "$3"/config/cluster.json \
               --cluster "${CLUSTER_OPTS}" \
               $triggeroptions \
               --keep-going --restart-times 3 -j 500 --rerun-incomplete --stats "$3"/logfiles/runtime_statistics.json \
@@ -224,7 +224,7 @@ function submit(){
             --output "$3"/logfiles/snakemake.log --error "$3"/logfiles/snakemake.log \
             snakemake --latency-wait 120 -s "$3"/workflow/Snakefile -d "$3" \
               --use-singularity --singularity-args "'-B $4'" --configfile="$3"/config.json \
-              --printshellcmds --cluster-config "$3"/resources/cluster.json \
+              --printshellcmds --cluster-config "$3"/config/cluster.json \
               --cluster "${CLUSTER_OPTS}" \
               $triggeroptions \
               --keep-going --restart-times 3 -j 500 --rerun-incomplete --stats "$3"/logfiles/runtime_statistics.json \

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -28,7 +28,7 @@ tmpdir   = config['options']['tmp_dir']          # Temporary directory
 # threads, mem, walltimes, etc.
 # TODO: Add handler for when the
 # mode is set to local.
-with open(join('resources', 'cluster.json')) as fh:
+with open(join('config', 'cluster.json')) as fh:
     cluster = json.load(fh)
 
 # Check for SE or PE FastQ files:

diff --git a/workflow/rules/build.smk b/workflow/rules/build.smk
@@ -80,7 +80,7 @@ workdir:OUTDIR
 # threads, mem, walltimes, etc.
 # TODO: Add handler for when the
 # mode is set to local.
-with open(join(OUTDIR, 'resources', 'build_cluster.json')) as fh:
+with open(join(OUTDIR, 'config', 'cluster.json')) as fh:
     cluster = json.load(fh)
 
 # Ensures backwards compatibility