Commit 9e17f00b authored by van den Berg's avatar van den Berg
Browse files

Add version directly, instead of relying on git

parent f69efaa1
[submodule "slurm-cluster-status"]
path = slurm-cluster-status
url = https://github.com/LUMC/slurm-cluster-status
......@@ -21,10 +21,8 @@ containers = {
settings=config["settings"]
# Determine version of HAMLET from git
out = subprocess.Popen(['git', 'describe', '--tags'], stdout=subprocess.PIPE)
stdout, stderr = out.communicate()
PIPELINE_VERSION = stdout.strip().decode('utf-8')
# The version of HAMLET
PIPELINE_VERSION = "v1.0.2-dev-1"
RUN_NAME = settings.get("run_name") or f"hamlet-{uuid4().hex[:8]}"
......
Subproject commit f9eafd882170e7cca228d2bbf580e28f7790ced6
__default__:
job_name: hamlet
queue: short
vmem: 4G
threads: 1
time: 00:10:00
tmp: 1G
exon_cov:
vmem: 4G
threads: 1
time: 00:30:00
align_flt3:
vmem: 4G
threads: 3
align_kmt2a:
vmem: 4G
threads: 3
align_vars:
vmem: 2G
threads: 8
aln_stats:
vmem: 10G
threads: 1
annotate_vars:
vmem: 1G
threads: 8
call_vars:
vmem: 4G
threads: 3
fastqc_raw:
vmem: 4G
threads: 4
fastqc_processed:
vmem: 4G
threads: 4
fusioncatcher:
vmem: 2G
threads: 8
insert_stats:
vmem: 16G
threads: 1
reorder_aln_header:
vmem: 16G
threads: 1
rna_stats:
vmem: 16G
threads: 1
sort_bamfile:
vmem: 16G
threads: 1
star_fusion:
vmem: 8G
threads: 8
time: 00:30:00
extract_sc_kmt2a:
vmem: 10G
threads: 3
count_raw_bases:
vmem: 20G
threads: 1
count_bases_exon:
vmem: 12G
threads: 1
count_bases_gene:
vmem: 10G
threads: 1
idsort_aln:
vmem: 10G
threads: 1
cluster: ' sbatch --parsable --job-name={jobid} --time={cluster.time} --partition={cluster.queue} --cpus-per-task={cluster.threads} --mem-per-cpu={cluster.vmem} --tmp={cluster.tmp}'
cluster-config: 'slurm-test/cluster.yaml'
cluster-status: 'slurm-cluster-status/slurm-cluster-status.py'
singularity-args: ' --containall --bind /exports'
singularity-prefix: '/exports/sasc-testing/singularity/snakemake_prefix'
use-singularity: true
jobs: 70
latency-wait: 120
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