just copy input fasta if in mask mode

tools/FROGS_filter_affiliation/FROGS_filter_affiliation.rule.snakefile

@@ -37,7 +37,8 @@ rule <step_name>__FROGS_filter_affiliation:
         {params.max_blast_evalue} \
         {params.min_blast_identity} \
         {params.min_blast_coverage}
-        echo \"1\t./{params.stepDir}/filtAff_report.html\" > {params.outDir}/text.generic.tsv
+        echo \"1\t./{params.stepDir}/filtAff_report.html\" > {params.outDir}/text.generic.tsv;
+        if [ "{params.output_mode}" == "--mask" ]; cp {input.fasta} {params.outDir}/affiFilter_sequences.fasta fi;
         """
 
         # {params.taxonomic_ranks} \
\ No newline at end of file

tools/FROGS_filter_affiliation/FROGS_filter_affiliation.yaml

@@ -24,23 +24,13 @@
           [
             { name: "biom_filtered", file: "affiFilter_abundance.biom", type: "biom", description: "the abundance file with filtered affiliation"},
             #sequence file is produced only in delete mode
-            #{ name: "sequence_file", file: "affiFilter_sequences.fasta", type: "fasta_file", description: "the filtered sequences"},
+            { name: "sequence_file", file: "affiFilter_sequences.fasta", type: "fasta_file", description: "the filtered sequences"},
             { name: "impacted", file: "impacted.tsv", type: "tsv", description: "The list of the OTUs deleted or hidden or with updated blast affiliation"},
             { name: "multihit", file: "impacted.multihit.tsv", type: "tsv", description: "The list of blast affiliations for multi-affiliated impacted OTU"},
             { name: "summary", file: "report_mqc.html", type: "html", description: "summary"}
           ],
         options:
           [
-            # {
-            #   name: FROGS_filter_affiliation_threads,
-            #   prefix: "",
-            #   type: numeric,
-            #   value: 4,
-            #   min: 1,
-            #   max: NA,
-            #   step: 1,
-            #   label: "Number of threads to use",
-            # },
             {
               name: FROGS_filter_affiliation_mode,
               prefix: "",