Merge branch 'gmap-2014-12-23' into 'devel'

Revert back to gmap 2014 12 23

See merge request !6

includes/snv-indels/Snakefile

@@ -3,12 +3,12 @@ from os import path
 # We need the QC-seq output
 include: "../qc-seq/Snakefile"
 
-localrules: plot_vars, table_vars_all, table_vars_hi
+localrules: 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",

test/test_expression.yml

@@ -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}'

test/test_snv_indels.yml

@@ -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: