add skip_smncopynumbercaller

nf-core · Jun 24, 2024 · 391f8c9 · 391f8c9
1 parent 38edf8a
commit 391f8c9
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Showing 4 changed files with 24 additions and 13 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,13 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- A new parameter `skip_smncopynumbercaller` to skip smncopynumbercaller module[#574](https://github.com/nf-core/raredisease/pull/574)
 - A new parameter `skip_sv_calling` to skip sv calling workflow [#572](https://github.com/nf-core/raredisease/pull/572)
 - Two new parameters `skip_snv_calling` and `skip_repeat_analysis` to skip snv calling and repeat analysis respectively [#571](https://github.com/nf-core/raredisease/pull/571)
 - Two new parameters `mbuffer_mem` and `samtools_sort_threads` to control resources given to mbuffer and samtools sort in the bwameme module [#570](https://github.com/nf-core/raredisease/pull/570)
 
 ### `Changed`
 
-- Remove several skip parameters that had been included in the pipeline to avoid failed CI tests [#574](https://github.com/nf-core/raredisease/pull/574)
+- Remove several skip parameters that had been included in the pipeline to avoid failed CI tests (see parameters table below) [#574](https://github.com/nf-core/raredisease/pull/574)
 - `readcount_intervals` parameter is now mandatory for running germlinecnvcaller. [#570](https://github.com/nf-core/raredisease/pull/570)
 - Turn off CNVnator, TIDDIT, SMNCopyNumberCaller, Gens, and Vcf2cytosure for targeted analysis [#573](https://github.com/nf-core/raredisease/pull/573)
 
@@ -24,17 +25,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter   | New parameter         |
-| --------------- | --------------------- |
-|                 | mbuffer_mem           |
-|                 | samtools_sort_threads |
-|                 | skip_repeat_analysis  |
-|                 | skip_snv_calling      |
-|                 | skip_sv_calling       |
-| skip_eklipse    |                       |
-| skip_fastqc     |                       |
-| skip_haplocheck |                       |
-| skip_qualimap   |                       |
+| Old parameter   | New parameter            |
+| --------------- | ------------------------ |
+|                 | mbuffer_mem              |
+|                 | samtools_sort_threads    |
+|                 | skip_repeat_analysis     |
+|                 | skip_snv_calling         |
+|                 | skip_sv_calling          |
+| skip_eklipse    |                          |
+| skip_fastqc     |                          |
+| skip_haplocheck |                          |
+| skip_qualimap   |                          |
+|                 | skip_smncopynumbercaller |
 
 ## 2.1.0 - Obelix [2024-05-29]
 

diff --git a/nextflow.config b/nextflow.config
@@ -35,6 +35,7 @@ params {
     skip_me_annotation         = false
     skip_mt_annotation         = false
     skip_repeat_analysis       = false
+    skip_smncopynumbercaller   = false
     skip_snv_annotation        = false
     skip_snv_calling           = false
     skip_sv_annotation         = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -553,6 +553,11 @@
                     "description": "Specifies whether or not to skip calling and annotation of repeat expansions.",
                     "fa_icon": "fas fa-toggle-on"
                 },
+                "skip_smncopynumbercaller": {
+                    "type": "boolean",
+                    "description": "Specifies whether or not to skip smncopynumbercaller.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "skip_snv_annotation": {
                     "type": "boolean",
                     "description": "Specifies whether or not to skip annotate SNV subworkflow.",

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -90,6 +90,9 @@ if (!params.skip_gens) {
     mandatoryParams += ["gens_gnomad_pos", "gens_interval_list", "gens_pon_female", "gens_pon_male"]
 }
 
+if (!params.skip_smncopynumbercaller) {
+    mandatoryParams += ["genome"]
+}
 for (param in mandatoryParams.unique()) {
     if (params[param] == null) {
         println("params." + param + " not set.")
@@ -693,7 +696,7 @@ workflow RAREDISEASE {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-    if ( params.analysis_type.equals("wgs") ) {
+    if ( params.analysis_type.equals("wgs") && !params.skip_smncopynumbercaller ) {
         RENAME_BAM_FOR_SMNCALLER(ch_mapped.genome_marked_bam, "bam").output
             .collect{it}
             .toList()