Modifiying quantifier param to make it more scalable

nf-core · Jan 10, 2025 · d1f406e · d1f406e
1 parent 6c6e7ec
commit d1f406e
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Showing 4 changed files with 37 additions and 11 deletions.
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -26,6 +26,6 @@ params {
     barcode_format       = "10X_3v3"
 
     split_amount         = 500000
-    quantifier           = "both"
+    quantifier           = "isoquant,oarfish"
 
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -207,8 +207,8 @@
                 },
                 "quantifier": {
                     "type": "string",
-                    "description": "Describe which quantification tool to use",
-                    "enum": ["oarfish", "isoquant", "both"]
+                    "description": "Provide a comma-delimited options of quantifiers for the pipeline to use. Options: (isoquant, oarfish)",
+                    "pattern": "^(oarfish|isoquant)(,(oarfish|isoquant))*$"
                 }
             },
             "required": ["quantifier"],

diff --git a/subworkflows/local/process_longread_scrna.nf b/subworkflows/local/process_longread_scrna.nf
@@ -23,13 +23,14 @@ workflow PROCESS_LONGREAD_SCRNA {
         fastq        // channel: [ val(meta), path(fastq) ]
         rseqc_bed    // channel: [ val(meta), path(rseqc_bed) ]
         read_bc_info // channel: [ val(meta), path(read_barcode_info) ]
+        quant_list   // list: List of quantifiers to use
 
         skip_save_minimap2_index // bool: Skip saving the minimap2 index
         skip_qc                  // bool: Skip qc steps
         skip_rseqc               // bool: Skip RSeQC
         skip_bam_nanocomp        // bool: Skip Nanocomp
-        quantifier               // str: Quantifier
         skip_seurat              // bool: Skip seurat qc steps
+        skip_dedup               // bool: Skip umitools deduplication
         split_umitools_bam       // bool: Skip splitting on chromsome for umitools
 
     main:
@@ -87,7 +88,7 @@ workflow PROCESS_LONGREAD_SCRNA {
         ch_dedup_log = Channel.empty()
         ch_idxstats = Channel.empty()
 
-        if (!params.skip_dedup) {
+        if (!skip_dedup) {
             UMITOOLS_DEDUP_SPLIT(
                 fasta,
                 fai,
@@ -115,7 +116,8 @@ workflow PROCESS_LONGREAD_SCRNA {
 
         ch_gene_qc_stats = Channel.empty()
         ch_transcript_qc_stats = Channel.empty()
-        if (quantifier.equals("oarfish")) {
+
+        if (quant_list.contains("oarfish")) {
             QUANTIFY_SCRNA_OARFISH (
                 ch_bam,
                 ch_bai,
@@ -126,7 +128,9 @@ workflow PROCESS_LONGREAD_SCRNA {
             )
             ch_versions = ch_versions.mix(QUANTIFY_SCRNA_OARFISH.out.versions)
             ch_transcript_qc_stats = QUANTIFY_SCRNA_OARFISH.out.transcript_qc_stats
-        } else {
+        } 
+
+        if (quant_list.contains("isoquant")) {
             QUANTIFY_SCRNA_ISOQUANT (
                 ch_bam,
                 ch_bai,

diff --git a/workflows/scnanoseq.nf b/workflows/scnanoseq.nf
@@ -4,6 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+// Whitelist
 if (params.whitelist) {
     blaze_whitelist = params.whitelist
 }
@@ -16,6 +17,25 @@ else {
     }
 }
 
+// Quantifiers
+
+// Associate the quantifiers with the kind of alignment needed
+GENOME_QUANT_OPTS = [ 'isoquant' ]
+TRANSCRIPT_QUANT_OPTS = [ 'oarfish' ]
+
+genome_quants = []
+transcript_quants = []
+for (quantifier in params.quantifier.split(',')) {
+    if (quantifier in GENOME_QUANT_OPTS) {
+        genome_quants.add(quantifier)
+    }
+
+    if (quantifier in TRANSCRIPT_QUANT_OPTS) {
+        transcript_quants.add(quantifier)
+    }
+}
+
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CONFIG FILES
@@ -389,20 +409,21 @@ workflow SCNANOSEQ {
 
     ch_multiqc_finalqc_files = Channel.empty()
 
-    if (params.quantifier.equals('isoquant') || params.quantifier.equals('both')){
+    if (genome_quants){
         PROCESS_LONGREAD_SCRNA_GENOME(
             genome_fasta,
             genome_fai,
             gtf,
             ch_extracted_fastq,
             ch_rseqc_bed,
             ch_corrected_bc_info,
+            genome_quants,
             params.skip_save_minimap2_index,
             params.skip_qc,
             params.skip_rseqc,
             params.skip_bam_nanocomp,
-            'isoquant',
             params.skip_seurat,
+            params.skip_dedup,
             true
         )
         ch_versions = ch_versions.mix(PROCESS_LONGREAD_SCRNA_GENOME.out.versions)
@@ -444,20 +465,21 @@ workflow SCNANOSEQ {
         )
     }
 
-    if (params.quantifier.equals('oarfish') || params.quantifier.equals('both')){
+    if (transcript_quants) {
         PROCESS_LONGREAD_SCRNA_TRANSCRIPT (
             transcript_fasta,
             transcript_fai,
             gtf,
             ch_extracted_fastq,
             ch_rseqc_bed,
             ch_corrected_bc_info,
+            transcript_quants,
             params.skip_save_minimap2_index,
             params.skip_qc,
             true,
             params.skip_bam_nanocomp,
-            'oarfish',
             params.skip_seurat,
+            true,
             false
         )