Added update to task rqcfilter outputs to fix issue #37

microbiomedata · Aug 15, 2024 · e251bc4 · kaijli · Aug 21, 2024 · e251bc4
1 parent 550d939
commit e251bc4
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Showing 3 changed files with 1 addition and 3 deletions.
diff --git a/longReadsqc.wdl b/longReadsqc.wdl
@@ -11,7 +11,6 @@ workflow LongReadsQC{
     String  log_level='INFO'
     Boolean rmdup = true
     Boolean overwrite = true
-    Boolean interleaved
     File?   reference
     String  pbmarkdup_container="microbiomedata/pbmarkdup:1.0"
     String  bbtools_container="microbiomedata/bbtools:39.01"

diff --git a/rqcfilter.wdl b/rqcfilter.wdl
@@ -28,7 +28,6 @@ workflow rqcfilter{
             file = input_files[0],
             proj = proj,
             reference = reference,
-            interleaved = interleaved
         }
     }
 

diff --git a/shortReadsqc.wdl b/shortReadsqc.wdl
@@ -246,7 +246,7 @@ task rqcfilter {
             File stat = filename_stat
             File stat2 = filename_stat2
             File info_file = filename_reproduce
-            File filtered = glob("filtered/*fastq.gz")[0]
+            File filtered = glob("filtered/*.anqdpht.fastq.gz")[0]
             File json_out = filename_stat_json
      }
 }