Do not run SAGE append germline for Neo

nf-core · Sep 9, 2024 · 8b15c62 · 8b15c62
1 parent ef7db8c
commit 8b15c62
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/subworkflows/local/sage_append/main.nf b/subworkflows/local/sage_append/main.nf
@@ -21,6 +21,9 @@ workflow SAGE_APPEND {
     genome_fai       // channel: [mandatory] /path/to/genome_fai
     genome_dict      // channel: [mandatory] /path/to/genome_dict
 
+    // Params
+    run_germline     // boolean: [mandatory] Run germline flag
+
     main:
     // Channel for version.yml files
     // channel: [ versions.yml ]
@@ -63,7 +66,7 @@ workflow SAGE_APPEND {
             def has_smlv_germline = file(purple_dir).resolve("${tumor_dna_id}.purple.germline.vcf.gz")
             def has_existing = Utils.hasExistingInput(meta, Constants.INPUT.SAGE_APPEND_VCF_NORMAL)
 
-            runnable: has_normal_dna && has_tumor_rna && has_smlv_germline && !has_existing
+            runnable: has_normal_dna && has_tumor_rna && has_smlv_germline && !has_existing && run_germline
             skip: true
                 return meta
         }

diff --git a/workflows/targeted.nf b/workflows/targeted.nf
@@ -478,6 +478,7 @@ workflow TARGETED {
             ref_data.genome_version,
             ref_data.genome_fai,
             ref_data.genome_dict,
+            true,  // run_germline
         )
 
         ch_versions = ch_versions.mix(SAGE_APPEND.out.versions)

diff --git a/workflows/wgts.nf b/workflows/wgts.nf
@@ -478,6 +478,7 @@ workflow WGTS {
             ref_data.genome_version,
             ref_data.genome_fai,
             ref_data.genome_dict,
+            run_config.stages.orange,  // run_germline [run for ORANGE but not Neo]
         )
 
         ch_versions = ch_versions.mix(SAGE_APPEND.out.versions)