Fix csvtk grep command for several contigs

genepi · Jan 10, 2024 · 6676083 · 6676083
1 parent a44e3be
commit 6676083
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Showing 4 changed files with 25 additions and 6 deletions.
diff --git a/modules/local/calculate_statistics.nf b/modules/local/calculate_statistics.nf
@@ -20,7 +20,7 @@ process CALCULATE_STATISTICS {
 
     ## calculate summary statistics
     samtools coverage ${bam_file} > samtools_coverage_${bam_file.baseName}.txt
-    csvtk grep -t -f3 -p 16569 samtools_coverage_${bam_file.baseName}.txt -T -o mtdna.txt
+    csvtk grep -t -f3 -p 16569 -C '\$' samtools_coverage_${bam_file.baseName}.txt -T -o mtdna.txt
 
     contig=\$(csvtk cut -t -f 1 mtdna.txt)
     numreads=\$(csvtk cut -t -f 4 mtdna.txt)

diff --git a/tests/data/bam/mitohpc/sample_S.bam b/tests/data/bam/mitohpc/sample_S.bam
diff --git a/tests/mitocalling.nf.test b/tests/mitocalling.nf.test
@@ -21,6 +21,25 @@ nextflow_pipeline {
             assert snapshot(path("${launchDir}/out/variants_ann.txt")).match()
         }
 
+    }
+
+    test("Runs with BAM file including different header contigs") {
+
+        when {
+            params {
+               project = "test-job"
+               files = "$projectDir/tests/data/bam/mitohpc/*bam"
+               mode = "mutserve"
+               output = "out"
+               output_reports = "reports"
+               output_auxiliary = "files"
+            }
+        }
+
+        then {
+            assert snapshot(path("${launchDir}/out/variants_ann.txt")).match()
+        }
+
     }
 
         test("Runs with single BAM file and mutect2") {

diff --git a/tests/mitocalling.nf.test.snap b/tests/mitocalling.nf.test.snap
@@ -1,14 +1,14 @@
 {
-    "Runs with single BAM file and mutect2": {
+    "Runs with BAM file including different header contigs": {
         "content": [
-            "variants_ann.txt:md5,accf5a353be01302f95b001338cf554a"
+            "variants_ann.txt:md5,c2aa6c45193a921f4a20238fe9bf6cd8"
         ],
-        "timestamp": "2023-12-21T13:01:38.349898"
+        "timestamp": "2024-01-10T13:45:32.689184313"
     },
     "Runs with single BAM file and mutserve": {
         "content": [
-            "variants_ann.txt:md5,64598b248689e6225c554b5d32c1bbd9"
+            "variants_ann.txt:md5,606016ca87ca11897119066253d53c62"
         ],
-        "timestamp": "2023-12-21T10:15:48.759709"
+        "timestamp": "2024-01-10T13:47:14.24639646"
     }
 }