Resucite lumpy-sv tool (#693)

* undeprecate lumpy_sv * upgrade dependencies * fix wrapper errors and lint python code * Update lumpy.xml * update tests * increase MAX_FILE_SIZE to 2M * suppress the -e lumpy option
ARTbio · Jul 8, 2024 · 37c0f09 · 37c0f09
1 parent 8cca5f0
commit 37c0f09
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Showing 13 changed files with 58 additions and 100 deletions.
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -16,7 +16,7 @@ env:
   GALAXY_FORK: galaxyproject
   GALAXY_BRANCH: release_23.2
   MAX_CHUNKS: 4
-  MAX_FILE_SIZE: 1M
+  MAX_FILE_SIZE: 2M
 concurrency:
   # Group runs by PR, but keep runs on the default branch separate
   # because we do not want to cancel ToolShed uploads

diff --git a/deprecated/lumpy_sv/test-data/output_extended.vcf b/deprecated/lumpy_sv/test-data/output_extended.vcf
diff --git a/deprecated/lumpy_sv/.shed.yml → tools/lumpy_sv/.shed.yml b/deprecated/lumpy_sv/.shed.yml → tools/lumpy_sv/.shed.yml
diff --git a/...ated/lumpy_sv/extractSplitReads_BwaMem.py → tools/lumpy_sv/extractSplitReads_BwaMem.py b/...ated/lumpy_sv/extractSplitReads_BwaMem.py → tools/lumpy_sv/extractSplitReads_BwaMem.py
@@ -21,7 +21,7 @@ def extractSplitsFromBwaMem(inFile, numSplits, includeDups, minNonOverlap):
             continue
         for el in sam.tags:
             if "SA:" in el:
-                if(len(el.split(";"))) <= numSplits:
+                if (len(el.split(";"))) <= numSplits:
                     split = 1
                     mate = el.split(",")
                     mateCigar = mate[3]
@@ -103,7 +103,6 @@ def extractCigarOps(cigar, flag):
         cigarOps = []
         for opString in cigarOpStrings:
             cigarOpList = atomicCigarSearch.findall(opString)
-#            print cigarOpList
             # "struct" for the op and it's length
             cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
             # add to the list of cigarOps
@@ -120,8 +119,7 @@ def extractCigarOps(cigar, flag):
             cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
             # add to the list of cigarOps
             cigarOps.append(cigar)
-#            cigarOps = cigarOps
-    return(cigarOps)
+    return cigarOps
 
 
 def calcQueryPosFromCigar(cigarOps):
@@ -202,7 +200,8 @@ def main():
                       help='''Include alignments marked as duplicates.
                       Default=False''')
     parser.add_option("-m", "--minNonOverlap", dest="minNonOverlap",
-                      default=20, type="int", help='''minimum non-overlap between
+                      default=20, type="int",
+                      help='''minimum non-overlap between
                       split alignments on the query (default=20)''',
                       metavar="INT")
     (opts, args) = parser.parse_args()