fix tmpdir being set

TMPDIR env variable should be used as default, not altered

binchicken/binchicken.py

@@ -1111,7 +1111,7 @@ def add_general_snakemake_options(argument_group, required_conda_prefix=False):
         retries_default = 3
         argument_group.add_argument("--cluster-retries", help=f"Number of times to retry a failed job when using cluster submission (see `--snakemake-profile`) [default: {retries_default}].", default=retries_default)
         argument_group.add_argument("--snakemake-args", help="Additional commands to be supplied to snakemake in the form of a space-prefixed single string e.g. \" --quiet\"", default="")
-        argument_group.add_argument("--tmp-dir", help="Path to temporary directory. [default: Use path from TMPDIR env variable]")
+        argument_group.add_argument("--tmp-dir", help="Path to temporary directory. [default: no default]")
 
     def add_base_arguments(argument_group):
         argument_group.add_argument("--forward", "--reads", "--sequences", nargs='+', help="input forward/unpaired nucleotide read sequence(s)")
@@ -1328,8 +1328,6 @@ def load_variable(variable):
         args.aviary_gtdbtk_db = load_variable("GTDBTK_DATA_PATH")
     if not hasattr(args, "aviary_checkm2_db") or not args.aviary_checkm2_db:
         args.aviary_checkm2_db = load_variable("CHECKM2DB")
-    if not args.tmp_dir:
-        args.tmp_dir = load_variable("TMPDIR")
 
     if hasattr(args, "genomes"):
         if not (args.genomes or args.genomes_list):

binchicken/config/template_coassemble.yaml

@@ -34,5 +34,5 @@ test: false
 mock_sra: false
 aviary_dryrun: false
 conda_prefix: false
-tmpdir: "/tmp"
+tmpdir: false
 build: false

binchicken/config/template_evaluate.yaml

@@ -5,4 +5,4 @@ original_bins: ""
 checkm_version: 2
 min_completeness: 70
 max_contamination: 10
-tmpdir: "/tmp"
+tmpdir: false

binchicken/workflow/coassemble.smk

@@ -695,7 +695,7 @@ rule aviary_assemble:
         drymkdir = "&& mkdir -p "+output_dir+"/coassemble/{coassembly}/assemble/assembly" if config["aviary_dryrun"] else "",
         drytouch = "&& touch "+output_dir+"/coassemble/{coassembly}/assemble/assembly/final_contigs.fasta" if config["aviary_dryrun"] else "",
         conda_prefix = config["conda_prefix"] if config["conda_prefix"] else ".",
-        tmpdir = config["tmpdir"],
+        tmpdir = f"TMPDIR={config["tmpdir"]}" if config["tmpdir"] else "",
     threads: lambda wildcards, attempt: get_assemble_threads(wildcards, attempt)
     resources:
         mem_mb = lambda wildcards, attempt: get_assemble_memory(wildcards, attempt, unit="MB"),
@@ -712,7 +712,7 @@ rule aviary_assemble:
         "EGGNOG_DATA_DIR=. "
         "CONDA_ENV_PATH={params.conda_prefix} "
         "SINGLEM_METAPACKAGE_PATH=. "
-        "TMPDIR={params.tmpdir} "
+        "{params.tmpdir} "
         "aviary assemble "
         "--coassemble "
         "-1 {params.reads_1} "
@@ -746,7 +746,7 @@ rule aviary_recover:
         fast = "--workflow recover_mags_no_singlem --skip-binners maxbin concoct rosella --skip-abundances --refinery-max-iterations 0" if config["aviary_speed"] == FAST_AVIARY_MODE else "",
         snakemake_profile = f"--snakemake-profile {config['snakemake_profile']}" if config["snakemake_profile"] else "",
         cluster_retries = f"--cluster-retries {config['cluster_retries']}" if config["cluster_retries"] else "",
-        tmpdir = config["tmpdir"],
+        tmpdir = f"TMPDIR={config["tmpdir"]}" if config["tmpdir"] else "",
     localrule: True
     threads:
         int(config["aviary_recover_threads"])
@@ -764,7 +764,7 @@ rule aviary_recover:
         "EGGNOG_DATA_DIR=. "
         "CONDA_ENV_PATH={params.conda_prefix} "
         "SINGLEM_METAPACKAGE_PATH={params.singlem_metapackage} "
-        "TMPDIR={params.tmpdir} "
+        "{params.tmpdir} "
         "aviary recover "
         "--assembly {input.assembly} "
         "-1 {params.reads_1} "