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hem
hamlet
Commits
9e17f00b
Commit
9e17f00b
authored
Mar 09, 2021
by
van den Berg
Browse files
Add version directly, instead of relying on git
parent
f69efaa1
Changes
5
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.gitmodules
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9e17f00b
[submodule "slurm-cluster-status"]
path = slurm-cluster-status
url = https://github.com/LUMC/slurm-cluster-status
Snakefile
View file @
9e17f00b
...
...
@@ -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]}"
...
...
slurm-cluster-status
@
f9eafd88
Compare
f9eafd88
...
f9eafd88
Subproject commit f9eafd882170e7cca228d2bbf580e28f7790ced6
slurm-test/cluster.yaml
deleted
100644 → 0
View file @
f69efaa1
__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
slurm-test/config.yaml
deleted
100644 → 0
View file @
f69efaa1
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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