Adding md5-sums to the test-yml-files

tests/test_annotation.yml

@@ -41,7 +41,15 @@
       # test_VEP.summary.html changes md5sums on reruns.
       contains:
         [
-          '<h3 id="gen_stats">General statistics</h3><table class="stats_table"><tr><td>Lines of input read</td><td>0</td></tr><tr><td>Variants processed</td><td>0</td></tr><tr><td>Variants filtered out</td><td>0</td></tr><tr><td>Novel / existing variants</td><td>-</td></tr><tr><td>Overlapped genes</td><td>0</td></tr><tr><td>Overlapped transcripts</td><td>0</td></tr><tr><td>Overlapped regulatory features</td><td>0</td></tr></table>',
+          "<tr><td>Input file</td><td>test_snpEff.ann.vcf.gz</td></tr><tr><td>Output file</td><td>test_snpEff_VEP.ann.vcf</td></tr>",
+          "General statistics",
+          "Lines of input read",
+          "Variants processed",
+          "Variants filtered out",
+          "Novel / existing variants",
+          "Overlapped genes",
+          "Overlapped transcripts",
+          "Overlapped regulatory features",
         ]
 - name: Run snpEff followed by VEP
   command: nextflow run main.nf -profile test,annotation --tools merge --skip_tools multiqc
@@ -59,7 +67,15 @@
       # test_snpEff_VEP.summary.html changes md5sums on reruns.
       contains:
         [
-          '<h3 id="gen_stats">General statistics</h3><table class="stats_table"><tr><td>Lines of input read</td><td>0</td></tr><tr><td>Variants processed</td><td>0</td></tr><tr><td>Variants filtered out</td><td>0</td></tr><tr><td>Novel / existing variants</td><td>-</td></tr><tr><td>Overlapped genes</td><td>0</td></tr><tr><td>Overlapped transcripts</td><td>0</td></tr><tr><td>Overlapped regulatory features</td><td>0</td></tr></table>',
+          "<tr><td>Input file</td><td>test_snpEff.ann.vcf.gz</td></tr><tr><td>Output file</td><td>test_snpEff_VEP.ann.vcf</td></tr>",
+          "General statistics",
+          "Lines of input read",
+          "Variants processed",
+          "Variants filtered out",
+          "Novel / existing variants",
+          "Overlapped genes",
+          "Overlapped transcripts",
+          "Overlapped regulatory features",
         ]
     - path: results/annotation/test/test_snpEff.ann.vcf.gz
       should_exist: false

tests/test_tools.yml

@@ -150,29 +150,29 @@
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz_control.cpn
       md5sum: 508a003da85b186d9a60d867ef7cdf15
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt
-      md5sum: 94bf84d58c9696f116a9a6d8cb350e14
+      md5sum: 9abc164091e5e330ea0198a99c8deaea
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_BAF.txt
-      md5sum: 8ff0fe03f03f715ee533be84eec8eff5
+      md5sum: 4c1540648d0d7dc0cfe5e3e37942d108
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_CNVs
-      md5sum: 7fa21a187466579fa532d6d40d7412cf
+      md5sum: 71f7dee6f22e1bab3c8ec10245508576
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_info.txt
       md5sum: 271271719c576d9218bdc859850e54ee
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph
       md5sum: 5d3321af93678f16878d59e01d3a87d3
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.txt
-      md5sum: 0565ec12db85fb2a84b2072563f27bba
+      md5sum: d78e65a7eba953c67b1cd6f9f6d31972
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn
       md5sum: befe1706c61464635a76c7323a6bd2a2
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png
-      md5sum: fb311638c98bf227bf95a29c48659d74
+      md5sum: 99c949fbc14c8a86bdf55552ad3dc35c
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png
       md5sum: 2eea2f34e6d05a6da3a8ec23e7075068
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png
       md5sum: 2f1565c565bd6b2306173f6efb916304
     - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz
       md5sum: f541e71aad4942260996107edaaed477
     - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz
-      md5sum: 83654d978b33d00687672c652eeeade7
+      md5sum: 262e13f9ebca61253c24416b5d8ff467
     - path: results/cnvkit
       should_exist: false
 - name: Run variant calling on somatic samples with controlfreec without intervals
@@ -1685,7 +1685,7 @@
     - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.TsTv.qual
       md5sum: bc68ae4e688e9fb772b457069e604883
     - path: results/variant_calling/tiddit/sample3/sample3.tiddit.ploidies.tab
-      md5sum: 0f01874e20df10ecc7418d4537c7aa82
+      md5sum: d65f8aa5bb136f77c23264640481f047
     - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz
       md5sum: 1aeb97037b73251bb79e48b355026c9d
     - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz.tbi
@@ -1723,7 +1723,7 @@
     - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.TsTv.qual
       md5sum: bc68ae4e688e9fb772b457069e604883
     - path: results/variant_calling/tiddit/sample1/sample1.tiddit.ploidies.tab
-      md5sum: 0f01874e20df10ecc7418d4537c7aa82
+      md5sum: d65f8aa5bb136f77c23264640481f047
     - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz
       md5sum: 72cd7a6dc9dece29fdcb0a19f69e1cb5
     - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz.tbi