Small bug fixes in kraken, geneext and generate_dashboard

bin/generate_dashboard.py

@@ -505,6 +505,10 @@ def get_val(source: Dict[str, Any], key: str, default: str = "N/A") -> Any:
 
         else:
             # alevin-fry fallback: require at least one of meta_info or quant.json to proceed
+            af_meta_file = find_file_for_sample(s_id, args.af_meta_info)
+            af_quant_file = find_file_for_sample(s_id, args.af_quant_json)
+            af_cell_meta_file = find_file_for_sample(s_id, args.af_cell_meta)
+
             af_meta = _safe_read_json(af_meta_file)
             af_quant = _safe_read_json(af_quant_file)
             af_cell = parse_cell_meta_tsv(af_cell_meta_file)

modules/local/tools/10x_saturate/plot_curve/main.nf

@@ -1,7 +1,7 @@
 process SATURATION_PLOT {
     publishDir "${params.outdir}/saturation/${meta.id}", mode: 'copy'
     tag "${meta.id}"
-    label 'process_single'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "oras://community.wave.seqera.io/library/pysam_samtools_matplotlib_numpy_pruned:b8f551e4a5153343"

modules/local/tools/10x_saturate/saturation_table/main.nf

@@ -1,7 +1,7 @@
 process SATURATION_TABLE {
     publishDir "${params.outdir}/saturation/${meta.id}", mode: 'copy'
     tag "${meta.id}"
-    label 'process_single'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "oras://community.wave.seqera.io/library/pysam_samtools_bc_python_pruned:82a1e27e868113f0"

modules/local/tools/kraken/kraken_classify/main.nf

@@ -29,7 +29,7 @@ process KRAKEN {
         --report ${meta.id}_kraken_taxonomy.txt \\
         --report-minimizer-data \\
         --use-names \\
-        --memory-mapping \
+        --memory-mapping \\
         --log ${meta.id}_kraken.log \\
         --output ${meta.id}_kraken_output.txt \\
         ${filtered_fasta}

subworkflows/local/mapping/mapping_starsolo.nf

@@ -159,17 +159,8 @@ workflow mapping_starsolo_workflow {
                     // Create STAR index with extended GTF
                     STARSOLO_INDEX_GENEEXT(GENE_EXT.out, ch_first_cDNA)
 
-                    // Join original data with the new sample-specific index
-                    data_output
-                        .join(STARSOLO_INDEX_GENEEXT.out)
-                        .multiMap { meta, f_cdna, f_umi, empty, sheet, index ->
-                            data_ch:  [meta, f_cdna, f_umi, empty, sheet]
-                            index_ch: [meta, index]
-                        }
-                        .set { ch_remap_inputs }
-
                     // Remap with STARsolo using the extended GTF
-                    STARSOLO_ALIGN_GENEEXT(ch_remap_inputs.data_ch, bc_whitelist, ch_remap_inputs.index_ch)
+                    STARSOLO_ALIGN_GENEEXT(data_output, bc_whitelist, STARSOLO_INDEX_GENEEXT.out)
                     SAMTOOLS_INDEX_GENEEXT(STARSOLO_ALIGN_GENEEXT.out.bam_file)
 
                     // Capture remapped STARsolo outputs