Commit ae33b468 authored by van den Berg's avatar van den Berg
Browse files

Update tests and revert gmap to 2014.12.23

parent 0d6f5970
Pipeline #3869 failed with stages
in 37 minutes
......@@ -8,7 +8,7 @@ localrules: plot_vars, table_vars_all, table_vars_hi
containers = {
"bedtools-2.27-grep-2.14-gawk-5.0-click-7-python-3.7": "docker://quay.io/biocontainers/mulled-v2-a4b89e0b16b1d7db92e5a069e5c40405b3b53aab:98c4ac2f0e27869be58f6a4d8bb7ae3bc02a3a70-0",
"debian": "docker://debian:buster-slim",
"gsnap": "docker://quay.io/biocontainers/gmap:2020.06.01--pl526h2f06484_0",
"gsnap": "docker://quay.io/biocontainers/gmap:2014.12.23--pl5.22.0_4",
"hamlet-scripts": "docker://lumc/hamlet-scripts:0.2",
"picard": "docker://quay.io/biocontainers/picard:2.20.5--0",
"python3": "docker://python:3.7.4-slim-stretch",
......
......@@ -72,21 +72,21 @@
contains:
- "exon\tHEL"
contains_regex:
- 'HMBS:119084882-119085066\t121\d{3}'
- 'HMBS:119084882-119085066\t12[01]\d{3}'
- 'MECOM:169083498-169085043\t211\d{3}'
- path: "HEL/expression/HEL.bases_per_gene"
contains:
- "gene\tHEL"
contains_regex:
- 'HMBS\t166\d{4}'
- 'MECOM\t70\d{4}'
- 'HMBS\t16[56]\d{4}'
- 'MECOM\t7[01]\d{4}'
- path: "HEL/expression/HEL.exon_ratios"
contains:
- "sample_name\texon\tcount\tratio\tabove_threshold\tdivisor_gene\tdivisor_exp"
contains_regex:
- 'HEL\tMECOM:169146722-169147734\t28\d{3}\t0.017\d*\tno\tHMBS\t166\d{4}'
- 'HEL\tMECOM:169146722-169147734\t28\d{3}\t0.017\d*\tno\tHMBS\t16[56]\d{4}'
- path: "HEL/expression/HEL.fragments_per_gene"
contains_regex:
......@@ -95,7 +95,7 @@
- path: "HEL/expression/HEL.raw_base"
contains_regex:
- 'chr11\t119084882\t119085066\t121\d{3}\t65\d\.\d*\tHMBS'
- 'chr11\t119084882\t119085066\t12[01]\d{3}\t65\d\.\d*\tHMBS'
- 'chr3\t169115382\t169116739\t17\d{4}\t128.\d*\tMECOM'
- name: test-expression-MECOM-vs-MECOM
......@@ -110,4 +110,4 @@
files:
- path: "HEL/expression/HEL.exon_ratios"
contains_regex:
- 'HEL\tMECOM:169146722-169147734\t28\d{3}\t0.04\d*\tyes\tMECOM\t70\d{4}'
- 'HEL\tMECOM:169146722-169147734\t28\d{3}\t0.04\d*\tyes\tMECOM\t7[01]\d{4}'
......@@ -85,19 +85,17 @@
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"
contains_regex:
- 'PAIR\t14266\t14266\t1\t0\t14\d{3}\t0.99\d{4}\t12\d{5}\t14\d{3}\t12\d{5}\t124\d{4}\t0\t0.00[2,3]\d{3}\t0.00[2,3]\d{3}\t0.000081\t92.4\d{5}\t14\d{3}\t0.99\d{4}'
- '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"
contains:
- "MEDIAN_INSERT_SIZE\tMODE_INSERT_SIZE\tMEDIAN_ABSOLUTE_DEVIATION\tMIN_INSERT_SIZE\tMAX_INSERT_SIZE\tMEAN_INSERT_SIZE\tSTANDARD_DEVIATION\tREAD_PAIRS\tPAIR_ORIENTATION"
contains_regex:
- '177\t128\t54\t31\t20794276\t200\.\d*\t106.4\d{5}\t699\d\tFR'
- path: "NB4/snv-indels/NB4.rna_stats"
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"
contains_regex:
- '1320386\t12[8,9]\d{4}\t0\t56\d{4}\t68\d{4}\t4[6,7]\d{3}\t50\d\t0\t0\t0\t2[7,8]\d{2}\t31\d{2}\t89'
- '1320386\t1[2,3]\d{5}\t0\t5\d{5}\t68\d{4}\t4[6,7]\d{3}\t37\d\t0\t0\t0\t2[7,8]\d{2}\t31\d{2}\t[8,9]\d'
- path: "NB4/snv-indels/NB4.variants_hi.csv"
contains:
......@@ -126,7 +124,6 @@
- path: "MV4-11/snv-indels/MV4-11.variants_hi.csv"
contains:
- "sample_id,gene_symbol,gene_id,CHROM,POS,REF,alleles,genotype,is_in_hotspot"
- "MV4-11,FLT3,ENSG00000122025,chr13,28034117,A,\"A,T\",A/T,yes"
- name: test-TET2-insertion-config
tags:
......
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