camper is not ready to use

Author: fischuu

CHANGELOG

@@ -3,6 +3,7 @@
 
 Version 0.3.*:
 --------------
+32: Adjusted the Output ruleset for contig_annotate__camper and moved from folder to concrete files
 31: Apply proteinortho now on the set of proteins obtains from the different MAG sets
 30: Added bakta annotation for each MAG separately instead of applying it to one dereplicated MAG-set only
 29: Summary tables for Diamond added

workflow/Snakefile

@@ -7,7 +7,7 @@ import pandas as pd
 import yaml
 import os
 
-version = "0.3.31"
+version = "0.3.32"
 
 # Import configuration files (as defined in the main configuration)
 params = yaml.load(open(config["params-file"], "r"), Loader=yaml.SafeLoader)

workflow/rules/contig_annotate/camper.smk

@@ -3,15 +3,17 @@ rule contig_annotate__camper__annotate:
     input:
         fa=CONTIG_PRODIGAL / "{assembly_id}/{assembly_id}.prodigal.fa",
     output:
-        annotation = directory(CONTIG_CAMPER / "{assembly_id}")
+        annotation = CONTIG_CAMPER / "{assembly_id}" / "annotations.tsv",
+        distillate = CONTIG_CAMPER / "{assembly_id}" / "distillate.tsv",
     log:
         CONTIG_CAMPER / "{assembly_id}.log",
     conda:
         "__environment__.yml"
     container:
         docker["camper"]
     params:
-        out_dir=CAMPER,
+        camper_dir = CONTIG_CAMPER,
+        out_dir = lambda wildcards: f"{CONTIG_CAMPER}/{wildcards.assembly_id}",
         camper_db=features["databases"]["camper"],
         nvme=config["nvme_storage"],
     threads: config["resources"]["cpu_per_task"]["multi_thread"]
@@ -26,24 +28,29 @@ rule contig_annotate__camper__annotate:
         cp {params.camper_db}/* {params.nvme} \
         2>> {log} 1>&2
         
+        tmpdir={params.out_dir}/tmp
+        
         camper_annotate -i {input} \
-                        -o {output} \
+                        -o $tmpdir \
                         --threads {threads} \
                         --camper_fa_db_loc {params.nvme}/CAMPER_blast.faa \
-	                --camper_fa_db_cutoffs_loc {params.nvme}/CAMPER_blast_scores.tsv \
-	                --camper_hmm_loc {params.nvme}/CAMPER.hmm  \
+	                      --camper_fa_db_cutoffs_loc {params.nvme}/CAMPER_blast_scores.tsv \
+	                      --camper_hmm_loc {params.nvme}/CAMPER.hmm  \
                         --camper_hmm_cutoffs_loc {params.nvme}/CAMPER_hmm_scores.tsv \
         2>> {log} 1>&2
 
-        camper_distill  -a {output}/annotations.tsv \
-                        -o {output}/distillate.tsv \
-	                --camper_distillate {params.nvme}/CAMPER_distillate.tsv \
+        camper_distill  -a $tmpdir/annotations.tsv \
+                        -o {output.distillate} \
+	                      --camper_distillate {params.nvme}/CAMPER_distillate.tsv \
 	      2>> {log} 1>&2
 	      
+	      # Move all tmp files one level up
+        mv "$tmpdir"/* {params.out_dir}/
+
         """
 
 
 rule contig_annotate__camper:
     """Run CAMPER on contig gene sequences."""
     input:
-         [CONTIG_CAMPER / f"{assembly_id}" for assembly_id in ASSEMBLIES],
+         [CONTIG_CAMPER / f"{assembly_id}" / "annotations.tsv" for assembly_id in ASSEMBLIES],