fixed typo in file output naming

Author: ilight1542

conf/modules.config

@@ -1662,7 +1662,7 @@ process {
         ext.args = [
             params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "", // Empty string since GATK complains if its default of -1 is provided.
         ].join(' ').trim()
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}_realigntarget" : "${sample_id}_${meta.reference}_realigntarget" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}_realigntarget" : "${meta.sample_id}_${meta.reference}_realigntarget" }
         publishDir = [
             enabled: false
         ]
@@ -1673,7 +1673,7 @@ process {
         ext.args = [
             params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "", // Empty string since GATK complains if its default of -1 is provided.
         ].join(' ').trim()
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}_realigned" : "${sample_id}_${meta.reference}_realigned" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}_realigned" : "${meta.sample_id}_${meta.reference}_realigned" }
         publishDir = [
             [
                 // data
@@ -1696,7 +1696,7 @@ process {
             "--genotype_likelihoods_model ${params.genotyping_gatk_ug_genotype_mode}",
             params.genotyping_gatk_ug_defaultbasequalities > 0 ? "--defaultBaseQualities ${params.genotyping_gatk_ug_defaultbasequalities}" : "", // Empty string since GATK complains if its default of -1 is provided.
         ].join(' ').trim() }
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}" : "${meta.sample_id}_${meta.reference}" }
         publishDir = [
             [
                 // data
@@ -1710,7 +1710,7 @@ process {
     withName: BCFTOOLS_INDEX_UG {
         tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
         ext.args = "--tbi" //tbi indices for consistency with GATK HC
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}" : "${meta.sample_id}_${meta.reference}" }
         publishDir = [
             [
                 // data
@@ -1730,7 +1730,7 @@ process {
             "--output-mode ${params.genotyping_gatk_hc_out_mode}",
             "--emit-ref-confidence ${params.genotyping_gatk_hc_emitrefconf}",
         ].join(' ').trim() }
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}" : "${meta.sample_id}_${meta.reference}" }
         publishDir = [
             [
                 // data
@@ -1748,7 +1748,7 @@ process {
             "-C ${params.genotyping_freebayes_min_alternate_count}",
             params.genotyping_freebayes_skip_coverage != 0 ? "-g ${params.genotyping_freebayes_skip_coverage}" : "",
         ].join(' ').trim() }
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}" : "${meta.sample_id}_${meta.reference}" }
         publishDir = [
             [
                 // data
@@ -1762,7 +1762,7 @@ process {
     withName: BCFTOOLS_INDEX_FREEBAYES {
         tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
         ext.args = "--tbi" //tbi indices for consistency with GATK HC
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}" : "${meta.sample_id}_${meta.reference}" }
         publishDir = [
             [
                 // data
@@ -1775,7 +1775,7 @@ process {
 
     withName: BCFTOOLS_STATS_GENOTYPING {
         tag = { params.genotyping_use_unmerged_libraries ? "${meta.reference}|${meta.sample_id}|${meta.library_id}" : "${meta.reference}|${meta.sample_id}" }
-        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${sample_id}_${meta.library_id}_${meta.reference}" : "${sample_id}_${meta.reference}" }
+        ext.prefix = { params.genotyping_use_unmerged_libraries ? "${meta.sample_id}_${meta.library_id}_${meta.reference}" : "${meta.sample_id}_${meta.reference}" }
         publishDir = [
             [
                 // stats