update mdsums

theiagen · Oct 21, 2024 · e23b19a · e23b19a
1 parent 7070c62
commit e23b19a
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml
@@ -232,7 +232,7 @@
       md5sum: 32c0be4fb7f3030bf9c74c0a836d4f2e
     - path: miniwdl_run/call-raw_check_reads/work/_miniwdl_inputs/0/ont.fastq.gz
     - path: miniwdl_run/call-stats_n_coverage/command
-      md5sum: 93414eacbbb9d7c4813bb54a8a507078
+      md5sum: 194a32a05aca8867a2d400465838945d
     - path: miniwdl_run/call-stats_n_coverage/inputs.json
       contains: ["bamfile", "samplename"]
     - path: miniwdl_run/call-stats_n_coverage/outputs.json
@@ -257,7 +257,7 @@
     - path: miniwdl_run/call-stats_n_coverage/work/ont.flagstat.txt
     - path: miniwdl_run/call-stats_n_coverage/work/ont.stats.txt
     - path: miniwdl_run/call-stats_n_coverage_primtrim/command
-      md5sum: c6e7de70dfdbb1858229e44777b84110
+      md5sum: 7246100df31a6508fe16757463e7c5a2
     - path: miniwdl_run/call-stats_n_coverage_primtrim/inputs.json
       contains: ["bamfile", "samplename"]
     - path: miniwdl_run/call-stats_n_coverage_primtrim/outputs.json

diff --git a/workflows/theiacov/wf_theiacov_clearlabs.wdl b/workflows/theiacov/wf_theiacov_clearlabs.wdl
@@ -215,7 +215,7 @@ workflow theiacov_clearlabs {
     Int number_Total = consensus_qc.number_Total
     Float percent_reference_coverage = consensus_qc.percent_reference_coverage
     # Percentage mapped reads
-    Float? percentage_mapped_reads = assembled_reads_percent.percentage_mapped
+    Float percentage_mapped_reads = stats_n_coverage.percentage_mapped_reads
     # SC2 specific coverage outputs
     Float? sc2_s_gene_mean_coverage = gene_coverage.sc2_s_gene_depth
     Float? sc2_s_gene_percent_coverage = gene_coverage.sc2_s_gene_percent_coverage