Merge pull request #178 from nf-core/grohmm-publishing

nf-core · Dec 2, 2024 · f071b81 · f071b81
2 parents e1e7f92 + 46964b2
commit f071b81
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Showing 4 changed files with 11 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#171](https://github.com/nf-core/nascent/pull/171) - Use assertAll in tests
 - [#165](https://github.com/nf-core/nascent/pull/165) - groHMM overhaul. Removed R mclapply calls and replaced with Nextflow scatter gather for parameter tuning. This creates a job for each parameter set.
 - [#174](https://github.com/nf-core/nascent/pull/174) - PINTS Scatter gather pattern by chromosome
+- [#178](https://github.com/nf-core/nascent/pull/178) - Remove groHMM parameter tuning publishing and remove `each` inputs from parameter tuning module
 
 ### Removed
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -367,7 +367,13 @@ process {
         ]
     }
 
-    withName: "GROHMM_.*" {
+    withName: "GROHMM_PARAMETERTUNING" {
+            publishDir = [
+                enabled: false
+            ]
+    }
+
+    withName: "GROHMM_TRANSCRIPTCALLING" {
         publishDir = [
             [
                 path: { "${params.outdir}/transcript_identification/grohmm" },

diff --git a/modules/local/grohmm/parametertuning/main.nf b/modules/local/grohmm/parametertuning/main.nf
@@ -9,10 +9,8 @@ process GROHMM_PARAMETERTUNING {
         'community.wave.seqera.io/library/grohmm:833aa94cad4202ac' }"
 
     input:
-    tuple val(meta), path(bams), path(bais)
+    tuple val(meta), path(bams), path(bais), val(UTS), val(LtProbB)
     path gxf
-    each UTS
-    each LtProbB
 
     output:
     tuple val(meta), path("*.tuning.csv"), emit: tuning

diff --git a/subworkflows/local/grohmm/main.nf b/subworkflows/local/grohmm/main.nf
@@ -27,10 +27,8 @@ workflow GROHMM {
     ch_ltprobb = channel.fromList((params.grohmm_min_ltprobb..params.grohmm_max_ltprobb).step(50))
 
     GROHMM_PARAMETERTUNING (
-        bams_bais,
-        gtf,
-        ch_uts,
-        ch_ltprobb,
+        bams_bais.combine(ch_uts).combine(ch_ltprobb),
+        gtf
     )
         .tuning
         .collectFile(