Add lulu for post clustering curation

tools/lulu/lulu.rule.snakefile

+rule <step_name>__lulu:
+    input:
+        **<step_name>__lulu_inputs(),
+    output: 
+        curated_table = config["results_dir"] + "/" + config["<step_name>__lulu_output_dir"] + "/curated_table.tsv",
+        otu_map = config["results_dir"] + "/" + config["<step_name>__lulu_output_dir"] + "/otu_map.tsv",
+    params: 
+        output_dir = config["results_dir"] + "/" + config["<step_name>__lulu_output_dir"]+ "/",
+        methode = config["<step_name>__lulu_matcher_method"],
+        minimum_ratio = config["<step_name>__lulu_minimum_ratio"],
+        minimum_match = config["<step_name>__lulu_minimum_match"],
+    log: 
+        config["results_dir"] + "/logs/" + config["<step_name>__lulu_output_dir"] + "/lulu_log.txt"
+    shell: 
+        """
+         if [ "{params.methode}" ==  "blast" ]
+         then
+            makeblastdb -in {input.sequence_file} -parse_seqids -dbtype nucl;
+            blastn -db {input.sequence_file} -outfmt '6 qseqid sseqid pident' -out {params.output_dir}/match_list.txt -qcov_hsp_perc 80 -perc_identity 84 -query {input.sequence_file} ;
+         else
+            vsearch --usearch_global {input.sequence_file} --db {input.sequence_file} --self --id .84 --iddef 1 --userout {params.output_dir}/match_list.txt -userfields query+target+id --maxaccepts 0 --query_cov .9 --maxhits 10
+         fi;
+
+        otutab={input.abundance_file};
+        matchlist={params.output_dir}/match_list.txt ;
+
+        Rscript --no-save - "{params.minimum_ratio}" "{params.minimum_match}" "{output.curated_table}" "{output.otu_map}" <<-E0F |& tee {log}
+        library(lulu)
+        cat("R loaded")
+        args <- commandArgs(TRUE)
+        cat("Script args are:")
+        args
+        otutab <- read.csv("$otutab",sep='\\t',header=TRUE,as.is=TRUE, row.names = 1)
+        matchlist <- read.table("$matchlist", header=FALSE,as.is=TRUE, stringsAsFactors=FALSE)
+        curated_result <- lulu(otutab, matchlist, minimum_ratio_type = "min", minimum_ratio = as.numeric(args[1]), minimum_match = as.numeric(args[2]), minimum_relative_cooccurence = 0.95)
+        write.table(curated_result\$curated_table, file=args[3] ,append = FALSE, quote = FALSE, sep = "\t", dec = ".", row.names = TRUE, col.names = NA)
+        write.table(curated_result\$otu_map, file=args[4] ,append = FALSE, quote = FALSE, sep = "\t", dec = ".", row.names = TRUE, col.names = NA)
+
+E0F 
+        """

tools/lulu/lulu.yaml

+{
+  id: lulu ,
+  name: lulu post clustering,
+  article: "https://www.nature.com/articles/s41467-017-01312-x",
+  website: "https://github.com/tobiasgf/lulu",
+  git: "https://github.com/tobiasgf/lulu",
+  description: "A r-package for distribution based post clustering curation of amplicon data.",
+  version: "latest",
+  documentation: "https://github.com/tobiasgf/lulu",
+  multiqc: "custom",
+  commands:
+    [
+      {
+        name: lulu,
+        cname: "lulu post clustering",
+        command: "",
+        category: "metabarcoding",
+        output_dir: lulu,
+        inputs: [
+          { name: "abundance_file", type: "tsv", file: "abundance.tsv", description: "OTU table with samples as columns and OTUs as rows, with unique OTU id's as row names" },
+          { name: sequence_file, type: "fasta_file", file: "OTU_seqs.fasta", description: "OTU sequences"},
+        ],
+        outputs:
+          [  
+            { name: curated_table, type: "tsv", file: "curated_table.tsv", description: "Table of retained OTUs" },
+            { name: otu_map, type: "tsv", file: "otu_map.tsv", description: "Table of information of which daughters were mapped to which parents OTUs" },
+          ],
+        options:
+          [
+            {
+              name: lulu_matcher_method,
+              type: radio,
+              value: "blast",
+              choices: [blast: blast, vsearch: vsearch],
+              label: "tool for pair wise matching of OTU sequences",
+            },
+            {
+              name: lulu_minimum_ratio,
+              type: numeric,
+              value: 1,
+              min: 0,
+              max: 1,
+              step: 0.01,
+              label: "minimim abundance ratio between a potential
+          error and a potential parent",
+            },
+            {
+              name: lulu_minimum_match,
+              type: numeric,
+              value: 84,
+              min: 0,
+              max: 100,
+              step: 1,
+              label: "minimum threshold (%)of sequence similarity for considering
+          any OTU as an error of another",
+            }
+          ],
+      },
+    ],
+  install: {
+      lulu: [
+        "Rscript -e 'devtools::install_github(\"tobiasgf/lulu\")' "
+      ],
+      VSEARCH: [
+        "cd /opt/biotools/",
+        " wget https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch-2.21.1-linux-x86_64.tar.gz",
+        " tar -zxvf vsearch-2.21.1-linux-x86_64.tar.gz",
+        " mv vsearch-2.21.1-linux-x86_64/bin/vsearch /opt/biotools/bin",
+        " rm -rf vsearch-2.21.1-linux-x86_64*"
+      ],
+      blast: [
+        "cd /opt/biotools/",
+        "wget -O ncbi-blast-2.12.0+.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz",
+        "tar -xvzf ncbi-blast-2.12.0+.tar.gz",
+        "ENV PATH $PATH:/opt/biotools/ncbi-blast-2.12.0+/bin"
+      ],
+  },
+  citations:  {
+    lulu: [
+      "Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications, 8(1), 1188."
+    ],
+  }
+}
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