add a parser for frna/cmo data from customised, unified, barcodes sam…

…plesheet

subworkflows/local/align_cellrangermulti.nf

@@ -57,9 +57,68 @@ workflow CELLRANGER_MULTI_ALIGN {
         ch_vdj_primer_index       = params.vdj_inner_enrichment_primers ? file(params.vdj_inner_enrichment_primers) : empty_file
         ch_beam_antigen_panel_csv = empty_file // currently not implemented
         ch_beam_control_panel_csv = empty_file // currently not implemented
-        // TODO: Add cellranger_multi_barcodes samplesheet parsing
-        ch_frna_sample_csv        = params.frna_sample_csv    ? file(params.frna_sample_csv)    : empty_file
-        ch_cmo_barcode_csv        = params.cmo_barcode_csv    ? file(params.cmo_barcode_csv)    : empty_file
+
+        // parse frna and barcode information
+        if (params.cellranger_multi_barcodes) {
+            Channel.fromPath( params.cellranger_multi_barcodes )
+            .splitCsv( header: true )
+            .map {
+                assert it.containsKey('sample'), "The ${params.cellranger_multi_barcodes} samplesheet for cellranger multi must contain a 'sample' colum. Please, check the docs."
+                assert it.containsKey('multiplexed_sample_id'), "The ${params.cellranger_multi_barcodes} samplesheet for cellranger multi must contain a 'multiplexed_sample_id' colum. Please, check the docs."
+                assert it.containsKey('description'), "The ${params.cellranger_multi_barcodes} samplesheet for cellranger multi must contain a 'description' colum. Please, check the docs."
+                assert it.containsKey('probe_barcode_ids') || it.containsKey('cmo_ids'), "The ${params.cellranger_multi_barcodes} samplesheet for cellranger multi must contain at least one, or both, of 'cmo_ids' or 'probe_barcode_ids' columns. Please, check the docs."
+
+                it
+            }
+            .branch {
+                cmo  : it.containsKey('cmo_ids')
+                frna : it.containsKey('probe_barcode_ids')
+            }
+            .set { ch_cellrangermulti_barcodes }
+
+            //
+            // Here, we parse the received cellranger multi barcodes samplesheet.
+            // We get the sample name information and merge the "sample-map" with the received GEX fastqs.
+            // The selection of the GEX fastqs is because samples are always expected to have at least GEX data.
+            // Then, using "joined" map, which means, the "additional barcode information" of each sample, we then,
+            // parse it to generate the cmo / frna samplesheets to be used by each sample.
+            //
+            // Here, because of the .join() we take advantage of the "FIFO"-rule and are sure that the data used in the
+            // module is from the same sample from the "normal" samplesheet.
+            //
+
+            // CMOs
+            ch_cmo_barcode_csv =
+            ch_grouped_fastq.gex.map{ it[0].id }
+            .join( ch_cellrangermulti_barcodes.cmo.collect().map{ [ it[0].sample, it ] }.groupTuple(by:0), remainder: true )
+            .map{ sample, meta ->
+                if (meta) {
+                    lines = [ 'sample,cmo_ids,description' ]
+                    meta[0].each{ lines = lines + [ "$it.sample,$it.cmo_ids,$it.description" ] }
+                    cmos = file( "${sample}_cmo_samplesheet.csv" )
+                    cmos.text = lines.join("\n").trim().toString()
+                    cmos
+                } else { empty_file }
+            }
+
+            // FRNAs
+            ch_frna_sample_csv =
+            ch_grouped_fastq.gex.map{ it[0].id }
+            .join( ch_cellrangermulti_barcodes.frna.collect().map{ [ it[0].sample, it ] }.groupTuple(by:0), remainder: true )
+            .map{ sample, meta ->
+                if (meta) {
+                    lines = [ 'sample,probe_barcode_ids,description' ]
+                    meta[0].each{ lines = lines + [ "$it.sample,$it.probe_barcode_ids,$it.description" ] }
+                    cmos = file( "${sample}_cmo_samplesheet.csv" )
+                    cmos.text = lines.join("\n").trim().toString()
+                    cmos
+                } else { empty_file }
+            }
+
+        } else {
+            ch_cmo_barcode_csv = empty_file
+            ch_frna_sample_csv = empty_file
+        }
 
         //
         // Prepare GTF