Latest funannotate biocontainer

Try to create Augustus tmp dir (possible workaround for nextgenusfs/funannotate#1149)

Author: TomHarrop

config/tools.yaml

@@ -27,7 +27,7 @@ tools:
     no_softmasking:
       - Vertebrates
   funannotate:
-    container: "docker://ghcr.io/tomharrop/container-funannotate:1.8.17_cv5"
+    container: "docker://ghcr.io/tomharrop/container-funannotate:1.8.17_cv6"
     result_files:
       - "funannotate.gff3"
     dbs:

extras/Makefile

@@ -3,5 +3,5 @@ test:
 	snakemake \
 		--configfile config/test.yaml \
 		--profile profiles/local \
-		--keep-going -n \
-		tiberius_target
+		--keep-going \
+		funannotate_target

workflow/rules/05_smk_hack.smk

@@ -6,6 +6,8 @@ logger.error("""
 *******************************
 """)
 
+
+# see https://github.com/snakemake/snakemake/issues/3916
 import json as _json
 _orig_dumps = _json.dumps
 def _dumps(obj, *args, **kwargs):

workflow/rules/31_funannotate.smk

@@ -55,7 +55,7 @@ rule funannotate_predict:
             Path("results", "run", "{genome}", "funannotate", "predict_results", x)
             for x in predict_result_files
         ),
-        directory(Path("results", "run", "{genome}", "funannotate", "predict_misc")),
+        predict_misc=directory(Path("results", "run", "{genome}", "funannotate", "predict_misc")),
     params:
         busco_lineage_name=subpath(input.busco_lineage, basename=True),
         busco_seed_species=lambda wildcards: genomes_dict[wildcards.genome][
@@ -81,6 +81,7 @@ rule funannotate_predict:
         tools_dict["funannotate"]["container"]
     shell:
         "env &> {log.env} && "
+        "mkdir -p {output.predict_misc}/tmp_opt_{wildcards.genome} && " # see https://github.com/nextgenusfs/funannotate/pull/1149
         'header_length=$( grep "^>" {input.fasta} | wc -L ) ; '
         "cp {input.gm_key} ${{HOME}}/.gm_key ; "
         "funannotate predict "