fixes #6

hundo/Snakefile

@@ -394,11 +394,16 @@ rule dereplicate_sequences_by_sample:
 
 rule combine_merged_reads:
     input:
-        expand("tmp/{sample}_dereplicated.fasta", sample=SAMPLES)
+        fastas = expand("tmp/{sample}_dereplicated.fasta", sample=SAMPLES)
     output:
-        "all-sequences.fasta"
-    shell:
-        "cat {input} > {output}"
+        fasta = "all-sequences.fasta"
+    run:
+        import shutil
+
+        with open(output.fasta, 'wb') as ofh:
+            for f in input.fastas:
+                with open(f, 'rb') as ifh:
+                    shutil.copyfileobj(ifh, ofh, 1024*1024*10)
 
 
 rule dereplicate_sequences:
@@ -1937,5 +1942,6 @@ rule report:
 
 
 onsuccess:
-    shutil.rmtree("tmp", ignore_errors=True)
+    if not config["no_temp_declared"]:
+        shutil.rmtree("tmp", ignore_errors=True)
     print("Protocol [%s] completed successfully." % PROTOCOL_VERSION)

hundo/__init__.py

@@ -1 +1 @@
-__version__ = "1.1.4"
+__version__ = "1.1.5"

hundo/hundo.py

@@ -356,6 +356,11 @@ def run_annotate(
     filter_contaminants = os.path.realpath(
         filter_contaminants) if filter_contaminants else ""
 
+    no_temp_declared = False
+    for sa in snakemake_args:
+        if sa == "--nt" or sa == "--notemp":
+            no_temp_declared = True
+
     cmd = ("snakemake --snakefile {snakefile} --directory {out_dir} "
            "--printshellcmds --jobs {jobs} --rerun-incomplete "
            "--nolock {conda} {dryrun} "
@@ -379,7 +384,8 @@ def run_annotate(
            "blast_minimum_bitscore={blast_minimum_bitscore} "
            "blast_top_fraction={blast_top_fraction} "
            "read_identity_requirement={read_identity_requirement} "
-           "prefilter_file_size={prefilter_file_size} {add_args} "
+           "prefilter_file_size={prefilter_file_size} "
+           "no_temp_declared={no_temp_declared} {add_args} "
            "{args}").format(
                snakefile=get_snakefile(),
                out_dir=os.path.realpath(out_dir),
@@ -410,6 +416,7 @@ def run_annotate(
                blast_top_fraction=blast_top_fraction,
                read_identity_requirement=read_identity_requirement,
                prefilter_file_size=prefilter_file_size,
+               no_temp_declared=no_temp_declared,
                add_args="" if snakemake_args and snakemake_args[
                    0].startswith("-") else "--",
                args=" ".join(snakemake_args))