From 1cd93d077bb873ec0da4b27771c11801711c954f Mon Sep 17 00:00:00 2001
From: AmstlerStephan <stephan.amstler@student.uibk.ac.at>
Date: Thu, 20 Jun 2024 13:07:35 +0200
Subject: [PATCH] add parser of mutserve output - adapt column names - filter
 for params.min_variant_level - Reduce number of columns (Sample, Pos,
 Reference, Variant, Variant-level)

---
 lib/processes/mutserve.nf                 | 11 ++++++++-
 tests/lib/processes/mutserve.nf.test.snap | 28 ++++++++++++++++++-----
 2 files changed, 32 insertions(+), 7 deletions(-)

diff --git a/lib/processes/mutserve.nf b/lib/processes/mutserve.nf
index a69384b..61181ca 100644
--- a/lib/processes/mutserve.nf
+++ b/lib/processes/mutserve.nf
@@ -11,8 +11,10 @@ process MUTSERVE {
     output:
       path "${type}.txt", emit: variants
       path "${type}_raw.txt", emit: variants_raw
+      path "${type}_parsed.txt", emit: variants_parsed
     
     script:
+    def min_variant_level = 0.0085
     """
       java -jar /opt/mutserve_LPA_adapted.jar call  \
       --output ${type}.vcf \
@@ -21,9 +23,16 @@ process MUTSERVE {
       --insertions \
       --deletions \
       --contig-name \$(awk '{ print \$1 }' ${bed}) \
-      ${bam}
+      ${bam} && \
+      echo -e "Sample\tPosition\tReference\tVariant\tVariant-level" > ${type}_parsed.txt && \
+      cat ${type}_raw.txt | \
+      tail +2 | \
+      awk -F'\t' 'NR==1 || (\$3 == \$4 && \$27 >= $min_variant_level) || \$3 != \$4' | \
+      awk -F'\t' '{print \$1, \$2, \$3, (\$3 == \$4 ? \$5 : \$4), (\$3 != \$4 ? \$25 : \$27)}' >> ${type}_parsed.txt
+
     """
 }
+// awk -F'\t' 'NR==1 || (\$3 != \$4 || \$3 == \$4 && \$27 >= $min_variant_level)' ${type}_raw.txt > ${type}_filtered.txt
 
 
 
diff --git a/tests/lib/processes/mutserve.nf.test.snap b/tests/lib/processes/mutserve.nf.test.snap
index 69c4b46..d5741f9 100644
--- a/tests/lib/processes/mutserve.nf.test.snap
+++ b/tests/lib/processes/mutserve.nf.test.snap
@@ -12,11 +12,21 @@
                     "final_raw.txt:md5,a647c13b88e318322308fa70526a8d96",
                     "final_raw.txt:md5,f8da170e2122c7caffa8fb3efb311434"
                 ],
+                "2": [
+                    "final_parsed.txt:md5,6acf8a7a7f2d4481996671da99ab520d",
+                    "final_parsed.txt:md5,f199bb8726d869d680004d35713cbdd4",
+                    "final_parsed.txt:md5,ff76e27a92d752db87135a57951f3cc4"
+                ],
                 "variants": [
                     "final.txt:md5,1e5554e27b3b8a0687374df975a6c9cb",
                     "final.txt:md5,871ecfddc44cb8b3aee5a3c482fa2900",
                     "final.txt:md5,bdcd9fa23bcd1e226b07988460f9b162"
                 ],
+                "variants_parsed": [
+                    "final_parsed.txt:md5,6acf8a7a7f2d4481996671da99ab520d",
+                    "final_parsed.txt:md5,f199bb8726d869d680004d35713cbdd4",
+                    "final_parsed.txt:md5,ff76e27a92d752db87135a57951f3cc4"
+                ],
                 "variants_raw": [
                     "final_raw.txt:md5,94352f26d9095f38eb44ff730db75dbc",
                     "final_raw.txt:md5,a647c13b88e318322308fa70526a8d96",
@@ -25,10 +35,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.0-rc2",
+            "nextflow": "24.05.0"
         },
-        "timestamp": "2024-03-11T12:49:45.12999"
+        "timestamp": "2024-06-20T13:06:51.2669"
     },
     "Should run without failures": {
         "content": [
@@ -39,18 +49,24 @@
                 "1": [
                     "final_raw.txt:md5,94352f26d9095f38eb44ff730db75dbc"
                 ],
+                "2": [
+                    "final_parsed.txt:md5,f199bb8726d869d680004d35713cbdd4"
+                ],
                 "variants": [
                     "final.txt:md5,1e5554e27b3b8a0687374df975a6c9cb"
                 ],
+                "variants_parsed": [
+                    "final_parsed.txt:md5,f199bb8726d869d680004d35713cbdd4"
+                ],
                 "variants_raw": [
                     "final_raw.txt:md5,94352f26d9095f38eb44ff730db75dbc"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.0-rc2",
+            "nextflow": "24.05.0"
         },
-        "timestamp": "2024-03-11T12:49:34.341905"
+        "timestamp": "2024-06-20T13:06:38.306114"
     }
 }
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