Adjust Neo to fit with alignment subworkflow

* add source selection for RNA BAM (samplesheet, alignment subworkflow) * use appropriate function call to determine present of RNA * relocate isofox_read_length assignment (wgts and targeted workflows)
nf-core · Mar 16, 2024 · 60f77d8 · 60f77d8
1 parent dcf2261
commit 60f77d8
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Showing 3 changed files with 28 additions and 13 deletions.
diff --git a/subworkflows/local/neo_prediction/main.nf b/subworkflows/local/neo_prediction/main.nf
@@ -13,6 +13,7 @@ workflow NEO_PREDICTION{
     take:
         // Sample data
         ch_inputs              // channel: [mandatory] [ meta ]
+        ch_tumor_rna_bam       // channel: [mandatory] [ meta, bam, bai ]
         ch_isofox              // channel: [mandatory] [ meta, isofox_dir ]
         ch_purple              // channel: [mandatory] [ meta, purple_dir ]
         ch_sage_somatic_append // channel: [mandatory] [ meta, sage_append_vcf ]
@@ -60,7 +61,7 @@ workflow NEO_PREDICTION{
         ch_finder_inputs_sorted = ch_finder_inputs_selected
             .branch { meta, purple_dir, linx_annotation_dir ->
 
-                def has_normal_dna = Utils.hasNormalDnaBam(meta)
+                def has_normal_dna = Utils.hasNormalDna(meta)
 
                 def has_runnable_inputs = purple_dir && linx_annotation_dir && has_normal_dna
 
@@ -103,13 +104,24 @@ workflow NEO_PREDICTION{
         //
         // Annotate the fusion-derived neoepitope using Isofox where RNA data is available
 
-        // Sort inputs
+        // Select input sources and sort
         // channel: runnable: [ meta, neo_finder_dir, tumor_bam_rna, tumor_bai_rna ]
         // channel: skip: [ meta ]
-        ch_isofox_inputs_sorted = ch_finder_out
-            .branch { meta, neo_finder_dir ->
-                runnable: Utils.hasTumorRnaBam(meta)
-                    return [meta, neo_finder_dir, Utils.getTumorRnaBam(meta), Utils.getTumorRnaBai(meta)]
+        ch_isofox_inputs_sorted = WorkflowOncoanalyser.groupByMeta(
+            ch_finder_out,
+            ch_tumor_rna_bam,
+        )
+            .map { meta, neo_finder_dir, tumor_bam, tumor_bai ->
+                return [
+                    meta,
+                    neo_finder_dir,
+                    Utils.selectCurrentOrExisting(tumor_bam, meta, Constants.INPUT.BAM_RNA_TUMOR),
+                    Utils.selectCurrentOrExisting(tumor_bai, meta, Constants.INPUT.BAI_RNA_TUMOR),
+                ]
+            }
+            .branch { meta, neo_finder_dir, tumor_bam, tumor_bai ->
+                runnable: Utils.hasTumorRna(meta)
+                    return [meta, neo_finder_dir, tumor_bam, tumor_bai]
                 skip: true
                     return meta
             }
@@ -125,7 +137,7 @@ workflow NEO_PREDICTION{
                     sample_id: Utils.getTumorDnaSampleName(meta),
                 ]
 
-                return [meta_isofox, neo_finder_dir, Utils.getTumorRnaBam(meta), Utils.getTumorRnaBai(meta)]
+                return [meta_isofox, neo_finder_dir, tumor_bam_rna, tumor_bai_rna]
             }
 
         // Run process
@@ -171,7 +183,7 @@ workflow NEO_PREDICTION{
                     cancer_type: meta[Constants.InfoField.CANCER_TYPE],
                 ]
 
-                if (Utils.hasTumorRnaBam(meta)) {
+                if (Utils.hasTumorRna(meta)) {
                     meta_scorer.sample_rna_id = Utils.getTumorRnaSampleName(meta)
                 }
 

diff --git a/workflows/targeted.nf b/workflows/targeted.nf
@@ -46,8 +46,10 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Check mandatory parameters
 if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
-// Create Path objects for some input files
+// Initial some subworkflow input parameters
 linx_gene_id_file = params.linx_gene_id_file ? file(params.linx_gene_id_file) : []
+// Used in Isofox subworkflow only
+isofox_read_length = params.isofox_read_length !== null ? params.isofox_read_length : Constants.DEFAULT_ISOFOX_READ_LENGTH_TARGETED
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -190,7 +192,6 @@ workflow TARGETED {
 
         isofox_counts = params.isofox_counts ? file(params.isofox_counts) : panel_data.isofox_counts
         isofox_gc_ratios = params.isofox_gc_ratios ? file(params.isofox_gc_ratios) : panel_data.isofox_gc_ratios
-        isofox_read_length = params.isofox_read_length !== null ? params.isofox_read_length : Constants.DEFAULT_ISOFOX_READ_LENGTH_TARGETED
 
         isofox_gene_ids = params.isofox_gene_ids ? file(params.isofox_gene_ids) : panel_data.isofox_gene_ids
         isofox_tpm_norm = params.isofox_tpm_norm ? file(params.isofox_tpm_norm) : panel_data.isofox_tpm_norm

diff --git a/workflows/wgts.nf b/workflows/wgts.nf
@@ -48,8 +48,10 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Check mandatory parameters
 if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
 
-// Create Path objects for some input files
+// Initial some subworkflow input parameters
 linx_gene_id_file = params.linx_gene_id_file ? file(params.linx_gene_id_file) : []
+// Used in Isofox and Neo subworkflows
+isofox_read_length = params.isofox_read_length !== null ? params.isofox_read_length : Constants.DEFAULT_ISOFOX_READ_LENGTH_WTS
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -193,7 +195,6 @@ workflow WGTS {
 
         isofox_counts = params.isofox_counts ? file(params.isofox_counts) : hmf_data.isofox_counts
         isofox_gc_ratios = params.isofox_gc_ratios ? file(params.isofox_gc_ratios) : hmf_data.isofox_gc_ratios
-        isofox_read_length = params.isofox_read_length !== null ? params.isofox_read_length : Constants.DEFAULT_ISOFOX_READ_LENGTH_WTS
 
         ISOFOX_QUANTIFICATION(
             ch_inputs,
@@ -725,6 +726,7 @@ workflow WGTS {
 
         NEO_PREDICTION(
             ch_inputs,
+            ch_align_rna_tumor_out,
             ch_isofox_out,
             ch_purple_out,
             ch_sage_somatic_append_out,
@@ -736,7 +738,7 @@ workflow WGTS {
             hmf_data.ensembl_data_resources,
             hmf_data.neo_resources,
             hmf_data.cohort_tpm_medians,
-            params.isofox_read_length,
+            isofox_read_length,
         )
 
         ch_versions = ch_versions.mix(NEO_PREDICTION.out.versions)