add prefix with bbmap

workflow/rules/cobinning.smk

@@ -13,6 +13,7 @@ rule filter_contigs:
         temp("Intermediate/cobinning/filtered_contigs/{sample}.fasta"),
     params:
         min_length=config["cobining_min_contig_length"],
+        prefix= lambda wc: wc.sample+ config["cobinning_separator"]
     log:
         "logs/cobinning/filter_contigs/{sample}.log",
     conda:
@@ -22,8 +23,9 @@ rule filter_contigs:
         mem=config["simplejob_mem"],
         java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
     shell:
-        " reformat.sh in={input} "
-        " fastaminlen={params.min_length} "
+        " rename.sh in={input} "
+        " prefix={params.prefix} addprefix=t addunderscore=f"
+        " minscaf={params.min_length} "
         " out={output} "
         " overwrite=true "
         " -Xmx{resources.java_mem}G 2> {log} "
@@ -68,22 +70,11 @@ rule combine_contigs:
         "Intermediate/cobinning/{bingroup}/combined_contigs.fasta.gz",
     log:
         "logs/cobinning/{bingroup}/combine_contigs.log",
-    params:
-        seperator=config["cobinning_separator"],
-        samples=get_samples_of_bingroup,
-    threads: 1
-    run:
-        import gzip as gz
-
-        with gz.open(output[0], "wt") as fout:
-            for sample, input_fasta in zip(params.samples, input.fasta):
-                with open(input_fasta) as fin:
-                    for line in fin:
-                        # if line is a header add sample name
-                        if line[0] == ">":
-                            line = f">{sample}{params.seperator}" + line[1:]
-                        # write each line to the combined file
-                        fout.write(line)
+    conda:
+        "../envs/required_packages.yaml"
+    threads: config["simplejob_threads"],
+    shell:
+        " (cat {input} | pigz -p {threads} > {output} ) 2> {log}"
 
 
 rule minimap_index:
@@ -95,7 +86,7 @@ rule minimap_index:
         index_size="12G",
     resources:
         mem=config["mem"],  # limited num of fatnodes (>200g)
-    threads: 3
+    threads: config["simplejob_threads"],
     log:
         "logs/cobinning/{bingroup}/minimap_index.log",
     benchmark:
@@ -113,7 +104,7 @@ rule samtools_dict:
         dict="Intermediate/cobinning/{bingroup}/combined_contigs.dict",
     resources:
         mem=config["simplejob_mem"],
-        ttime=config["runtime"]["simplejob"],
+        time=config["runtime"]["simplejob"],
     threads: 1
     log:
         "logs/cobinning/{bingroup}/samtools_dict.log",
@@ -240,7 +231,7 @@ rule parse_vamb_output:
     input:
         expand(rules.run_vamb.output, bingroup=sampleTable.BinGroup.unique()),
     output:
-        renamed_clusters="Intermediate/cobinning/vamb_clusters.tsv.gz",
+        renamed_clusters="Binning/vamb/vamb_clusters.tsv.gz",
         cluster_atributions=expand(vamb_cluster_attribution_path, sample=SAMPLES),
     log:
         "logs/cobinning/vamb_parse_output.log",
@@ -257,7 +248,7 @@ rule parse_vamb_output:
 
 rule vamb:
     input:
-        "Intermediate/cobinning/vamb_clusters.tsv.gz",
+        "Binning/vamb/vamb_clusters.tsv.gz",
         expand("{sample}/binning/vamb/cluster_attribution.tsv", sample=SAMPLES),