As test_tsv mixes SE/PE switch to dedup-based workaround

Author: jfy133

.github/workflows/ci.yml

@@ -109,7 +109,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bam_filtering --bam_mapping_quality_threshold 37 --bam_discard_unmapped --bam_unmapped_type 'fastq'
       - name: DEDUPLICATION Test with dedup
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mergedonly --dedupper 'dedup'
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --dedupper 'dedup' --dedup_all_merged
       - name: GENOTYPING_HC Test running GATK HaplotypeCaller
         run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker --run_genotyping --genotyping_tool 'hc' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'