Added previous output as reference to the integration test.

Signed-off-by: Philip R. Kensche <p.kensche@dkfz-heidelberg.de>
DKFZ-ODCF · Mar 6, 2024 · 5ecc597 · 5ecc597
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Showing 123 changed files with 14 additions and 6 deletions.
diff --git a/test/test1_paired.bam → test/reference/test1_paired.bam b/test/test1_paired.bam → test/reference/test1_paired.bam
diff --git a/test/reference/test1_paired.bam_fastqs/default_R1.fastq.gz b/test/reference/test1_paired.bam_fastqs/default_R1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/default_R2.fastq.gz b/test/reference/test1_paired.bam_fastqs/default_R2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/default_S.fastq.gz b/test/reference/test1_paired.bam_fastqs/default_S.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/default_U1.fastq.gz b/test/reference/test1_paired.bam_fastqs/default_U1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/default_U2.fastq.gz b/test/reference/test1_paired.bam_fastqs/default_U2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_R1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_R1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_R2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_R2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_S.fastq.gz b/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_S.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_U1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_U1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_U2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run1_gerald_D1VCPACXX_1_U2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_R1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_R1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_R2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_R2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_S.fastq.gz b/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_S.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_U1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_U1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_U2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run2_gerald_D1VCPACXX_2_U2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_R1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_R1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_R2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_R2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_S.fastq.gz b/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_S.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_U1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_U1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_U2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run3_gerald_D1VCPACXX_3_U2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_R1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_R1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_R2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_R2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_S.fastq.gz b/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_S.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_U1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_U1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_U2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run4_gerald_D1VCPACXX_4_U2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_R1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_R1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_R2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_R2.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_S.fastq.gz b/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_S.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_U1.fastq.gz b/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_U1.fastq.gz
diff --git a/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_U2.fastq.gz b/test/reference/test1_paired.bam_fastqs/run5_gerald_D1VCPACXX_5_U2.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/default_R1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/default_R1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/default_R2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/default_R2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/default_S.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/default_S.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/default_U1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/default_U1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/default_U2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/default_U2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz
diff --git a/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz b/test/reference/test1_paired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz
diff --git a/test/test1_unpaired.bam → test/reference/test1_unpaired.bam b/test/test1_unpaired.bam → test/reference/test1_unpaired.bam
diff --git a/test/reference/test1_unpaired.bam_fastqs/default_R1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/default_R1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/default_R2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/default_R2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/default_S.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/default_S.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/default_U1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/default_U1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/default_U2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/default_U2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_R1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_R1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_R2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_R2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_S.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_S.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_U1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_U1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_U2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run1_gerald_D1VCPACXX_1_U2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_R1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_R1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_R2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_R2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_S.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_S.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_U1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_U1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_U2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run2_gerald_D1VCPACXX_2_U2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_R1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_R1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_R2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_R2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_S.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_S.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_U1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_U1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_U2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run3_gerald_D1VCPACXX_3_U2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_R1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_R1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_R2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_R2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_S.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_S.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_U1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_U1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_U2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run4_gerald_D1VCPACXX_4_U2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_R1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_R1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_R2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_R2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_S.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_S.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_U1.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_U1.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_U2.fastq.gz b/test/reference/test1_unpaired.bam_fastqs/run5_gerald_D1VCPACXX_5_U2.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/default_R1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/default_R1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/default_R2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/default_R2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/default_S.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/default_S.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/default_U1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/default_U1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/default_U2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/default_U2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_R2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_S.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run1_gerald_D1VCPACXX_1_U2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_R2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_S.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run2_gerald_D1VCPACXX_2_U2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_R2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_S.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run3_gerald_D1VCPACXX_3_U2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_R2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_S.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run4_gerald_D1VCPACXX_4_U2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_R2.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_S.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U1.sorted.fastq.gz
diff --git a/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz b/test/reference/test1_unpaired.bam_sorted_fastqs/run5_gerald_D1VCPACXX_5_U2.sorted.fastq.gz
diff --git a/test/test1.sh b/test/test1.sh
@@ -78,18 +78,18 @@ nextflow run "$workflowDir/main.nf" \
   -ansi-log \
   -resume \
   -work-dir "$outDir/work" \
-  --input="$workflowDir/test/test1_paired.bam,$workflowDir/test/test1_unpaired.bam" \
+  --input="$workflowDir/test/reference/test1_paired.bam,$workflowDir/test/reference/test1_unpaired.bam" \
   --outputDir="$outDir" \
   --sortFastqs=false \
   --compressorThreads=0 \
   --sortThreads=1 \
   --sortMemory="100 MB"
 assertEqual \
-  "$(readsInBam "$workflowDir/test/test1_paired.bam")" \
+  "$(readsInBam "$workflowDir/test/reference/test1_paired.bam")" \
   "$(readsInOutputDir "$outDir/test1_paired.bam_fastqs")" \
   "Read number in unsorted output FASTQs on paired-end input bam"
 assertEqual \
-  "$(readsInBam "$workflowDir/test/test1_unpaired.bam")" \
+  "$(readsInBam "$workflowDir/test/reference/test1_unpaired.bam")" \
   "$(readsInOutputDir "$outDir/test1_unpaired.bam_fastqs")" \
   "Read number in unsorted output FASTQs on single-end input bam"
 
@@ -98,19 +98,27 @@ nextflow run "$workflowDir/main.nf" \
   -ansi-log \
   -resume \
   -work-dir "$outDir/work" \
-  --input="$workflowDir/test/test1_paired.bam,$workflowDir/test/test1_unpaired.bam" \
+  --input="$workflowDir/test/reference/test1_paired.bam,$workflowDir/test/reference/test1_unpaired.bam" \
   --outputDir="$outDir" \
   --sortFastqs=true \
   --compressorThreads=0 \
   --sortThreads=1 \
   --sortMemory="100 MB"
 assertEqual \
-  "$(readsInBam "$workflowDir/test/test1_paired.bam")" \
+  "$(readsInBam "$workflowDir/test/reference/test1_paired.bam")" \
   "$(readsInOutputDir "$outDir/test1_paired.bam_sorted_fastqs")" \
   "Read number in sorted output FASTQs on paired-end input bam"
 assertEqual \
-  "$(readsInBam "$workflowDir/test/test1_unpaired.bam")" \
+  "$(readsInBam "$workflowDir/test/reference/test1_unpaired.bam")" \
   "$(readsInOutputDir "$outDir/test1_unpaired.bam_sorted_fastqs")" \
   "Read number in sorted output FASTQs on single-end input bam"
 
+for ref in reference/test*/*; do
+  out="$outDir/$(echo "$ref" | sed "s/reference//")"
+  assertEqual \
+    "$(zcat "$ref" | md5sum | cut -d' ' -f1)" \
+    "$(zcat "$out" | md5sum | cut -d' ' -f1)" \
+    "MD5 of $ref and $out"
+done
+
 testFinished