Add kmcp search

nf-core · Jul 27, 2023 · 29ea089 · 29ea089
1 parent c80dda4
commit 29ea089
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Showing 6 changed files with 5 additions and 222 deletions.
diff --git a/modules.json b/modules.json
@@ -116,16 +116,6 @@
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
-                    "kmcp/compute": {
-                        "branch": "master",
-                        "git_sha": "6a8df5472d224697a64502961291038fafc7ed08",
-                        "installed_by": ["modules"]
-                    },
-                    "kmcp/index": {
-                        "branch": "master",
-                        "git_sha": "1106a8046ead1562c57e1c969f8c66863cab338b",
-                        "installed_by": ["modules"]
-                    },
                     "kmcp/merge": {
                         "branch": "master",
                         "git_sha": "0fbbd07d2430dd2adcbdd2900bd420e10263c94a",

diff --git a/modules/nf-core/kmcp/compute/main.nf b/modules/nf-core/kmcp/compute/main.nf
diff --git a/modules/nf-core/kmcp/compute/meta.yml b/modules/nf-core/kmcp/compute/meta.yml
diff --git a/modules/nf-core/kmcp/index/main.nf b/modules/nf-core/kmcp/index/main.nf
diff --git a/modules/nf-core/kmcp/index/meta.yml b/modules/nf-core/kmcp/index/meta.yml
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
@@ -377,7 +377,7 @@ workflow PROFILING {
 
     if (params.run_kmcp) {
 
-            ch_input_for_kmcpcompute = ch_input_for_profiling.kmcp
+            ch_input_for_kmcp = ch_input_for_profiling.kmcp
                                 .filter {
                                     meta, reads, meta_db, db ->
                                         if ( meta['instrument_platform'] == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] Kmcp is only suitable for short-read metagenomic profiling, with much lower sensitivity on long-read datasets. Skipping kmcp for sample ${meta.id}."
@@ -386,17 +386,12 @@ workflow PROFILING {
                                     .multiMap {
                                     it ->
                                         reads: [ it[0] + it[2], it[1] ]
-                                        db: [ it[0], it[3] ]
-                                //.multiMap { meta, reads, meta_db, db ->
-                                //    reads:  [meta, reads.flatten()]
-                                //    db:     [meta, db ]
-                            }
+                                        db: it[3]
 
+                            }
 
-            KMCP_COMPUTE (ch_input_for_kmcpcompute.db)
-            KMCP_INDEX (KMCP_COMPUTE.out.outdir)
-            KMCP_SEARCH (KMCP_INDEX.out.kmcp.map{it[1]}, ch_input_for_kmcpcompute.reads)
-            //KMCP_PROFILE (KMCP_SEARCH.out.result,params.kmcp_taxdump, params.kmcp_taxid, params.kmcp_mode)
+            KMCP_SEARCH (ch_input_for_kmcp.db, ch_input_for_kmcp.reads)
+            //KMCP_PROFILE (KMCP_SEARCH.out.result,ch_input_for_kmcpcompute.db.map, params.kmcp_mode)
 
             //ch_versions = ch_versions.mix( KMCP_PROFILE.out.versions.first() )
             //ch_raw_profiles    = ch_raw_profiles.mix( KMCP_PROFILE.out.profile )