Updating mlst workflow

bio-raum · Sep 17, 2024 · 98309ab · 98309ab
1 parent 4dc846b
commit 98309ab
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Showing 3 changed files with 5 additions and 17 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -430,6 +430,7 @@ process {
         ]
     }
     withName: 'CHEWBBACA_ALLELECALL_SINGLE' {
+        ext.args = "--no-inferred"
         publishDir = [
             path: { "${params.outdir}/samples/${meta.sample_id}/chewbbaca" },
             mode: params.publish_dir_mode,
@@ -446,7 +447,7 @@ process {
 	]   
     }
     withName: 'CHEWBBACA_ALLELECALL' {
-
+        ext.args = "--no-inferred"
         publishDir = [
             path: { "${params.outdir}/cgMLST/chewbbaca/${meta.sample_id}" },
             mode: params.publish_dir_mode,

diff --git a/modules/chewbbaca/allelecall/main.nf b/modules/chewbbaca/allelecall/main.nf
@@ -22,7 +22,8 @@ process CHEWBBACA_ALLELECALL {
 
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: meta.sample_id
-    results = "results_${prefix}"
+    def db_name = file(db).getSimpleName()
+    results = "results_${prefix}_${db_name}"
 
     """
     chewBBACA.py AlleleCall \\

diff --git a/subworkflows/mlst/main.nf b/subworkflows/mlst/main.nf
@@ -154,21 +154,7 @@ workflow MLST_TYPING {
         )
         ch_versions = ch_versions.mix(CHEWBBACA_ALLELECALL_SINGLE.out.versions)
 
-        ch_profiles = CHEWBBACA_ALLELECALL_SINGLE.out.profile.map { m, r ->
-                def meta = [:]
-                meta.db_name = m.db_name
-                meta.sample_id = m.db_name
-                tuple(meta, r)
-            }.groupTuple()
-
-        /*
-        Join profiles, assuming we have more than one
-        */
-        //CHEWBBACA_JOINPROFILES(
-        //    ch_profiles.filter{ m,reports -> reports.size() > 1 }
-        //)
-        //ch_versions = ch_versions.mix(CHEWBBACA_JOINPROFILES.out.versions)
-
+
         /* Join assemblies and databases to generate
         [ meta, [ assemblies ], db ] and filter out all
         cases where # assemblies is < 3 (no point to compute relationships)