diff --git a/CHANGELOG.md b/CHANGELOG.md index d1f068e..699bfe6 100644 --- 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 b/config/cluster.json similarity index 84% rename from resources/cluster.json rename to config/cluster.json index 5869c03..f0b6f4a 100644 --- a/resources/cluster.json +++ b/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/${{SLURM_JOBID}}.%j.{rule}.{wildcards}.out", @@ -50,9 +50,13 @@ "threads": "16", "time": "1-00:00:00" }, + "qualimapinfo": { + "mem": "20g" + }, "rsem": { "gres": "lscratch:500", - "threads": "16", + "mem": "48g", + "threads": "32", "time": "1-00:00:00" }, "star1p": { @@ -78,6 +82,18 @@ "threads": "32", "time": "2-00:00:00" }, + "star_rl": { + "mem": "48g", + "gres": "lscratch:128", + "threads": "32", + "time": "12:00:00" + }, + "star_genome": { + "mem": "48g", + "gres": "lscratch:128", + "threads": "32", + "time": "12:00:00" + }, "arriba": { "gres": "lscratch:256", "mem": "110g", diff --git a/config/templates/project.json b/config/templates/project.json index 648fa51..b9d9113 100644 --- a/config/templates/project.json +++ b/config/templates/project.json @@ -6,7 +6,7 @@ "MINSAMPLES": "0.5", "annotation": "", "binset": "standard-bin", - "cluster": "resources/cluster.json", + "cluster": "config/cluster.json", "contrasts": { "rcontrasts": "" }, diff --git a/resources/build_cluster.json b/resources/build_cluster.json deleted file mode 100644 index 1d14dac..0000000 --- a/resources/build_cluster.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "__default__": { - "mem": "8g", - "gres": "lscratch:128", - "threads": "1", - "time": "4:00:00", - "partition": "norm", - "name": "{rule}.{wildcards}", - "output": "logfiles/slurmfiles/${{SLURM_JOBID}}.%j.{rule}.{wildcards}.out", - "error": "logfiles/slurmfiles/${{SLURM_JOBID}}.%j.{rule}.{wildcards}.err" - }, - "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" - }, - "rsem": { - "mem": "48g", - "threads": "32", - "time": "12:00:00" - }, - "qualimapinfo": { - "mem": "20g" - } -} diff --git a/resources/builder b/resources/builder index 862b937..2205b08 100755 --- 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 index 69ca4ec..69d8646 100755 --- 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 index 9259569..cead37f 100644 --- 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 index e3957a6..a9428c2 100644 --- 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