Commit ab41c2e5 authored by van den Berg's avatar van den Berg
Browse files

Remove brittle regex test for file content

These values tend to change with minor changes in the input data or tool
versions, and are overly hard to read due to the use of regular expressions.
For now, we only check the file content to make sure the headers haven't
changes.
parent e283f481
Pipeline #5283 failed with stages
in 11 seconds
...@@ -84,8 +84,6 @@ ...@@ -84,8 +84,6 @@
- path: "NB4/snv-indels/NB4.aln_stats" - path: "NB4/snv-indels/NB4.aln_stats"
contains: contains:
- "CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER" - "CATEGORY\tTOTAL_READS\tPF_READS\tPCT_PF_READS\tPF_NOISE_READS\tPF_READS_ALIGNED\tPCT_PF_READS_ALIGNED\tPF_ALIGNED_BASES\tPF_HQ_ALIGNED_READS\tPF_HQ_ALIGNED_BASES\tPF_HQ_ALIGNED_Q20_BASES\tPF_HQ_MEDIAN_MISMATCHES\tPF_MISMATCH_RATE\tPF_HQ_ERROR_RATE\tPF_INDEL_RATE\tMEAN_READ_LENGTH\tREADS_ALIGNED_IN_PAIRS\tPCT_READS_ALIGNED_IN_PAIRS\tPF_READS_IMPROPER_PAIRS\tPCT_PF_READS_IMPROPER_PAIRS\tBAD_CYCLES\tSTRAND_BALANCE\tPCT_CHIMERAS\tPCT_ADAPTER"
contains_regex:
- 'PAIR\t1426\d\t1426\d\t1\t0\t14\d{3}\t0.99\d{4}\t1[23]\d{5}\t14\d{3}\t1[23]\d{5}\t12\d{5}\t0\t0.00[2,3]\d{3}\t0.00[2,3]\d{3}\t0.000\d{3}\t92.\d{6}\t14\d{3}\t0.99\d{4}'
- path: "NB4/snv-indels/NB4.insert_stats" - path: "NB4/snv-indels/NB4.insert_stats"
contains: contains:
...@@ -94,8 +92,6 @@ ...@@ -94,8 +92,6 @@
- path: "NB4/snv-indels/NB4.rna_stats" - path: "NB4/snv-indels/NB4.rna_stats"
contains: contains:
- "PF_BASES\tPF_ALIGNED_BASES\tRIBOSOMAL_BASES\tCODING_BASES\tUTR_BASES\tINTRONIC_BASES\tINTERGENIC_BASES\tIGNORED_READS\tCORRECT_STRAND_READS\tINCORRECT_STRAND_READS\tNUM_R1_TRANSCRIPT_STRAND_READS\tNUM_R2_TRANSCRIPT_STRAND_READS\tNUM_UNEXPLAINED_READS" - "PF_BASES\tPF_ALIGNED_BASES\tRIBOSOMAL_BASES\tCODING_BASES\tUTR_BASES\tINTRONIC_BASES\tINTERGENIC_BASES\tIGNORED_READS\tCORRECT_STRAND_READS\tINCORRECT_STRAND_READS\tNUM_R1_TRANSCRIPT_STRAND_READS\tNUM_R2_TRANSCRIPT_STRAND_READS\tNUM_UNEXPLAINED_READS"
contains_regex:
- '1320386\t12[8,9]\d{4}\t0\t56\d{4}\t68\d{4}\t4[6,7]\d{3}\t(49|50)\d\t0\t0\t0\t2[7,8]\d{2}\t31\d{2}\t89'
- path: "NB4/snv-indels/NB4.variants_hi.csv" - path: "NB4/snv-indels/NB4.variants_hi.csv"
contains: contains:
......
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