mapping to transcriptome tested on full size dataset, bam_input on fullsize dataset still to do

Author: number-25

conf/test_full.config

@@ -18,9 +18,10 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data
-    input                           = "test/samplesheets/samplesheet_test_local.csv"
-    sequencing_type                 = "ont-drna" // sequencing molecule [ont-drna OR ont-cdna]
-    bam_input                       = false
+    //input                           = "test/samplesheets/samplesheet_test_local.csv"
+    input                           = "test/samplesheets/samplesheet_test_local_bam.csv"
+    sequencing_type                 = "ont-cdna" // sequencing molecule [ont-drna OR ont-cdna]
+    bam_input                       = true
     // Genome references
     // These channel names have to match those in the full workflow also
     genome_fasta                    = "assets/fulltest_data/hg38.analysisSet.fa.gz"

modules/local/minimap2/index/main.nf

@@ -1,5 +1,5 @@
 process MINIMAP2_INDEX {
-    tag "$fasta"
+    tag "$genome_fasta"
     label 'process_medium'
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/ngsbits/mapping_qc/main.nf

@@ -1,7 +1,6 @@
 process NGS_BITS {
     tag "$meta.id"
     label 'process_medium'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ngs-bits:2025_01--py313h6fdbb3c_0':

nextflow_schema.json

@@ -48,13 +48,7 @@
                     "description": "Skip the preparation of the reference files."
                 }
             },
-            "required": [
-                "genome_fasta",
-                "transcriptome_fasta",
-                "annotation_gtf",
-                "transcriptome_mapping",
-                "skip_prepare_reference"
-            ],
+            "required": ["genome_fasta", "transcriptome_fasta", "annotation_gtf"],
             "fa_icon": "fas fa-book-open"
         },
         "input_output_options": {
@@ -391,8 +385,7 @@
                     "type": "boolean",
                     "description": "Skip OARFISH transcript quantification."
                 }
-            },
-            "required": ["bam_input"]
+            }
         }
     },
     "allOf": [