Remove mmseqs/createindex module and update mmseqs/easysearch module

Author: Joon-Klaps

conf/modules.config

@@ -1344,20 +1344,10 @@ process {
             ]
         }
 
-        withName: MMSEQS_CREATEINDEX {
-            ext.args = '--search-type 2' // make sure search-type match easy-search
-            publishDir = [
-                path: { "${params.outdir}/databases/${meta.id}" },
-                mode: params.publish_dir_mode,
-                enabled: params.save_databases,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
         withName: MMSEQS_EASYSEARCH {
-            ext.args= '--search-type 2 --rescore-mode 3 --format-output query,target,theader,fident,qlen,tlen,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits' // don't change format-output
+            ext.args= { "--search-type ${params.mmseqs_searchtype} --rescore-mode 3 --format-output query,target,theader,fident,qlen,tlen,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits" } // don't change format-output
             publishDir = [
-                path: { "${params.outdir}/consensus_qc/${meta.sample}/mmseqs/" },
+                path: { "${params.outdir}/consensus_qc/mmseqs/"},
                 mode: params.publish_dir_mode,
                 pattern: "*.tsv",
                 saveAs: { filename -> params.prefix || params.global_prefix  ? "${params.global_prefix}-$filename" : filename }

modules.json

@@ -222,11 +222,6 @@
                         "git_sha": "18a43d316b6fd683dc2346867b42882b99811cfd",
                         "installed_by": ["modules"]
                     },
-                    "mmseqs/createindex": {
-                        "branch": "master",
-                        "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3",
-                        "installed_by": ["modules"]
-                    },
                     "mmseqs/createtsv": {
                         "branch": "master",
                         "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3",

modules/nf-core/custom/dumpsoftwareversions/main.nf

@@ -124,6 +124,7 @@ params {
     skip_alignment_qc           = false
     annotation_db               = "https://viralzone.expasy.org/resources/Virosaurus/2020%5F4/virosaurus90%5Fvertebrate-20200330.fas.gz"
     skip_annotation             = false
+    mmseqs_searchtype           = 3
 
     // Global
     prefix                      = null

modules/nf-core/mmseqs/createindex/environment.yml

@@ -779,7 +779,7 @@
                 },
                 "annotation_db": {
                     "type": "string",
-                    "default": "${projectDir}/assets/bv-brc-refvirus-anno.withRC.fasta.gz",
+                    "default": "https://viralzone.expasy.org/resources/Virosaurus/2020%5F4/virosaurus90%5Fvertebrate-20200330.fas.gz",
                     "fa_icon": "fas fa-database",
                     "description": "Database used for annotation of the cosensus constructs",
                     "help_text": "The metada fields are stored in the fasta comment as `key1:\"value1\"|key2:\"value2\"|...` see docs/databases.md for more information."
@@ -798,6 +798,13 @@
                     "type": "boolean",
                     "description": "Skip creating an alignment of each the collapsed clusters and each iterative step",
                     "fa_icon": "fas fa-forward"
+                },
+                "mmseqs_searchtype": {
+                    "type": "integer",
+                    "default": 3,
+                    "fa_icon": "fas fa-search",
+                    "description": "Specify the search algorithm to use for mmseqs. 0: auto 1: amino acid, 2: translated, 3: nucleotide, 4: translated nucleotide alignment",
+                    "help_text": "Only search-type 3 supports both forward and reverse search\n1 - BLASTP;\n2 - TBLASTN;\n3 - BLASTN;\n4 - TBLASTX"
                 }
             },
             "fa_icon": "fas fa-balance-scale"

modules/nf-core/mmseqs/createindex/main.nf

@@ -1,6 +1,5 @@
 
 include { MMSEQS_CREATEDB    as MMSEQS_CREATEANNOTATIONDB  } from '../../modules/nf-core/mmseqs/createdb/main'
-include { MMSEQS_CREATEINDEX                               } from '../../modules/nf-core/mmseqs/createindex/main'
 include { MMSEQS_EASYSEARCH                                } from '../../modules/nf-core/mmseqs/easysearch/main'
 
 workflow MMSEQS_ANNOTATE {
@@ -15,12 +14,8 @@ workflow MMSEQS_ANNOTATE {
     MMSEQS_CREATEANNOTATIONDB ( db )
     ch_versions = ch_versions.mix(MMSEQS_CREATEANNOTATIONDB.out.versions)
 
-    // create mmseqs index for faster reuse of the db
-    MMSEQS_CREATEINDEX ( MMSEQS_CREATEANNOTATIONDB.out.db )
-    ch_versions = ch_versions.mix(MMSEQS_CREATEINDEX.out.versions)
-
     // search the genomes against the annotation db
-    MMSEQS_EASYSEARCH ( genomes, MMSEQS_CREATEINDEX.out.db_indexed )
+    MMSEQS_EASYSEARCH ( genomes, MMSEQS_CREATEANNOTATIONDB.out.db )
     ch_versions = ch_versions.mix(MMSEQS_EASYSEARCH.out.versions.first())
 
     emit: