Add full test, enable binqc

assets/test_full_input.yaml

@@ -0,0 +1,10 @@
+tolid: xyTesTing1
+pacbio:
+  fasta:
+    - ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/014/SRR13128014/SRR13128014_subreads.fastq.gz
+hic:
+  cram:
+    - https://github.com/prototaxites/lrm_testdata/raw/refs/heads/main/hic.cram
+  enzymes:
+    - DpnII
+    - HinfI

conf/test_full.config

@@ -15,10 +15,6 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
-
-    // Fasta references
-    fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
+    // Input data
+    input  = "${baseDir}/assets/test_full_input.yaml"
 }

workflows/longreadmag.nf

@@ -14,6 +14,7 @@ include { BINNING                } from '../subworkflows/local/binning'
 include { BIN_REFINEMENT         } from '../subworkflows/local/bin_refinement'
 include { PREPARE_DATA           } from '../subworkflows/local/prepare_data'
 include { READ_MAPPING           } from '../subworkflows/local/read_mapping'
+include { BIN_QC                 } from '../subworkflows/local/bin_qc.nf'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -65,6 +66,11 @@ workflow LONGREADMAG {
 
             ch_bins = BINNING.out.bins
                 | mix(BIN_REFINEMENT.out.refined_bins)
+
+            if(params.enable_binqc) {
+                BIN_QC(ch_bins)
+                ch_versions = ch_versions.mix(BIN_QC.out.versions)
+            }
         }
     }
     //