Add version directly, instead of relying on git

.gitmodules

-[submodule "slurm-cluster-status"]
-	path = slurm-cluster-status
-	url = https://github.com/LUMC/slurm-cluster-status

Snakefile

@@ -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

-Subproject commit f9eafd882170e7cca228d2bbf580e28f7790ced6

slurm-test/cluster.yaml

-__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

-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