add motus preplong for long reads

nf-core · Dec 12, 2024 · 047808a · 047808a
1 parent 79055cd
commit 047808a
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Showing 9 changed files with 291 additions and 5 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -775,6 +775,13 @@ process {
         ]
     }
 
+    withName: MOTUS_PREPLONG {
+        tag = {"${meta.db_name}|${meta.id}"}
+        publishDir = [
+            enabled : false
+        ]
+    }
+
     withName: MOTUS_MERGE {
         ext.args = { params.standardisation_motus_generatebiom ? "-B" : "" }
         ext.prefix = { "motus_${meta.id}_combined_reports" }

diff --git a/modules.json b/modules.json
@@ -185,6 +185,11 @@
                         "git_sha": "3cf419b5480c5ca8893f5ea6e1746d2b3a7c326d",
                         "installed_by": ["modules"]
                     },
+                    "motus/preplong": {
+                        "branch": "master",
+                        "git_sha": "b56ac062cb5fa01ef3d76a05f44cc9d6f0234140",
+                        "installed_by": ["modules"]
+                    },
                     "motus/profile": {
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",

diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml
diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test
diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test.snap b/modules/nf-core/motus/preplong/tests/main.nf.test.snap
diff --git a/modules/nf-core/motus/preplong/tests/tags.yml b/modules/nf-core/motus/preplong/tests/tags.yml
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
@@ -14,6 +14,7 @@ include { KAIJU_KAIJU                                   } from '../../modules/nf
 include { KAIJU_KAIJU2TABLE as KAIJU_KAIJU2TABLE_SINGLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
 include { DIAMOND_BLASTX                                } from '../../modules/nf-core/diamond/blastx/main'
 include { MOTUS_PROFILE                                 } from '../../modules/nf-core/motus/profile/main'
+include { MOTUS_PREPLONG                                } from '../../modules/nf-core/motus/preplong/main'
 include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ                } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
 include { KMCP_SEARCH                                   } from '../../modules/nf-core/kmcp/search/main'
 include { KMCP_PROFILE                                  } from '../../modules/nf-core/kmcp/profile/main'
@@ -371,13 +372,27 @@ workflow PROFILING {
                                     if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] mOTUs currently does not accept FASTA files as input. Skipping mOTUs for sample ${it[0].id}."
                                     !it[0].is_fasta
                                 }
-                                .multiMap {
-                                    it ->
-                                        reads: [it[0] + it[2], it[1]]
-                                        db: it[3]
+                                .branch {
+                                    longread: it[0].instrument_platform == 'OXFORD_NANOPORE'
+                                    shortread: it[0].instrument_platform != 'OXFORD_NANOPORE'
                                 }
+        ch_input_for_motus_longread = ch_input_for_motus.longread
+                                        .multiMap {
+                                            it ->
+                                                reads:[it[0] + it[2], it[1]]
+                                                db: it[3]
+                                        }
+        ch_input_for_motus_shortread = ch_input_for_motus.shortread
+                                        .multiMap {
+                                            it ->
+                                                reads:[it[0] + it[2], it[1]]
+                                                db: it[3]
+                                        }
+        MOTUS_PREPLONG ( ch_input_for_motus_longread.reads, ch_input_for_motus_longread.db )
+
+        MOTUS_PROFILE ( MOTUS_PREPLONG.out.out.mix(ch_input_for_motus_shortread.reads), ch_input_for_motus_longread.db.mix(ch_input_for_motus_shortread.db) )
 
-        MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
+        //ch_versions        = ch_versions.mix( MOTUS_PREPLONG.out.versions.first() )
         ch_versions        = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
         ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )