Commit b96eba60 authored by khalid's avatar khalid
Browse files

just copy input fasta if in mask mode

parent b06eb584
...@@ -37,7 +37,8 @@ rule <step_name>__FROGS_filter_affiliation: ...@@ -37,7 +37,8 @@ rule <step_name>__FROGS_filter_affiliation:
{params.max_blast_evalue} \ {params.max_blast_evalue} \
{params.min_blast_identity} \ {params.min_blast_identity} \
{params.min_blast_coverage} {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} \ # {params.taxonomic_ranks} \
\ No newline at end of file
...@@ -24,23 +24,13 @@ ...@@ -24,23 +24,13 @@
[ [
{ name: "biom_filtered", file: "affiFilter_abundance.biom", type: "biom", description: "the abundance file with filtered affiliation"}, { name: "biom_filtered", file: "affiFilter_abundance.biom", type: "biom", description: "the abundance file with filtered affiliation"},
#sequence file is produced only in delete mode #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: "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: "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"} { name: "summary", file: "report_mqc.html", type: "html", description: "summary"}
], ],
options: 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, name: FROGS_filter_affiliation_mode,
prefix: "", prefix: "",
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment