Add support for multiple chromosome files for gene level analysis

modules/local/regenie_step2_gene_tests.nf

@@ -5,7 +5,7 @@ process REGENIE_STEP2_GENE_TESTS {
 
   input:
     path step1_out
-    tuple val(filename), path(genotyped_plink_file_bim), path(genotyped_plink_file_bed), path(genotyped_plink_file_fam)
+    tuple val(filename), path(genotyped_plink_file_bed), path(genotyped_plink_file_bim), path(genotyped_plink_file_fam)
     val assoc_format
 	  path phenotypes_file
     path covariates_file
@@ -39,11 +39,10 @@ process REGENIE_STEP2_GENE_TESTS {
     def writeMasks = params.regenie_write_bed_masks  ? "--write-mask" : ''
     def joint = params.regenie_gene_joint ? "--joint ${params.regenie_gene_joint}":''
     def condition_list = params.regenie_condition_list ? "--condition-list $condition_list_file" : ''
-
   """
   regenie \
     --step 2 \
-    $format ${genotyped_plink_file_bed} \
+    $format ${filename}${extension} \
     --phenoFile ${phenotypes_file} \
     --phenoColList  ${params.phenotypes_columns} \
     --bsize ${params.regenie_bsize_step2} \

workflows/nf_gwas.nf

@@ -222,12 +222,10 @@ workflow NF_GWAS {
 
       if (genotypes_association_format == 'bed') {
 
-//         Channel.fromFilePairs(genotypes_association).set {step2_gene_tests_ch}
-        Channel.fromFilePairs(genotypes_association)
-        .map {tuple(it[0].baseName, it[0], it[1], it[2])}
+        Channel.fromFilePairs(genotypes_association, size:3)
+        .map { tuple(it[1][0].baseName, it[1][0], it[1][1], it[1][2]) }
         .set {step2_gene_tests_ch}
 
-
       }
 
     }