adjust wdl to accomodate external sra fastq headers

docs/index.rst

@@ -6,7 +6,7 @@
          site the file is incorporated into. You can learn more about the `github_url` field at:
          https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#confval-github_url
 
-Reads QC Workflow (v1.0.14-alpha.1)
+Reads QC Workflow
 =============================
 
 .. image:: lrrqc_workflow2024.svg
@@ -39,6 +39,7 @@ The following parameters are used for :literal:`rqcfilter2` in this workflow::
  - removemouse=true    :  Remove mouse reads via mapping.
  - barcodefilter=false :  Disable improper barcodes filter
  - chastityfilter=false:  Remove illumina reads failing chastity filter.
+ - filterbytile=false :  Remove reads from low-quality parts of the flowcell. 
  - trimfragadapter=true:  Trim all known Illumina adapter sequences, including TruSeq and Nextera.
  - removemicrobes=true :  Remove common contaminant microbial reads via mapping, and place them in a separate file.
 

rqcfilter.wdl

@@ -14,6 +14,7 @@ workflow rqcfilter{
     Boolean        interleaved
     Boolean        shortRead
     Boolean?       chastityfilter_flag
+    Boolean?       filterbytile_flag
   }
 
     Boolean has_accessions = defined(accessions) && length(select_first([accessions, []])) > 0
@@ -42,7 +43,8 @@ workflow rqcfilter{
                 input_fq2 = if is_interleaved then [] else select_first([sra2fastq.output_fq2, input_fq2]),
                 interleaved = is_interleaved,
                 proj = proj,
-                chastityfilter_flag = if (has_accessions) then false else chastityfilter_flag
+                chastityfilter_flag = if (has_accessions) then false else chastityfilter_flag,
+                filterbytile_flag = if (has_accessions) then false else filterbytile_flag
         }
     }
 

shortReadsqc.wdl

@@ -15,6 +15,7 @@ workflow ShortReadsQC {
         String   database="/refdata/"
         Int      rqc_mem = 180
         Boolean? chastityfilter_flag
+        Boolean? filterbytile_flag
     }
 
     if (interleaved) {
@@ -43,7 +44,8 @@ workflow ShortReadsQC {
             database = database,
             memory = rqc_mem,
             container = bbtools_container,
-            chastityfilter_flag = chastityfilter_flag
+            chastityfilter_flag = chastityfilter_flag,
+            filterbytile_flag = filterbytile_flag
     }
 
     call stats_jsons {
@@ -183,6 +185,7 @@ task rqcfilter {
         String  database
         String  rqcfilterdata = database + "/RQCFilterData"
         Boolean chastityfilter_flag=true
+        Boolean filterbytile_flag=true
         Int     memory
         Int     xmxmem = floor(memory * 0.75)
         Int    threads
@@ -192,6 +195,7 @@ task rqcfilter {
         String  filename_stat2="filtered/filterStats2.txt"
         String  filename_reproduce="filtered/reproduce.sh"
         String chastityfilter= if (chastityfilter_flag) then "cf=t" else "cf=f"
+        String filterbytile = if (filterbytile_flag) then "filterbytile=t" else "filterbytile=f"
     }
 
     command <<<
@@ -221,6 +225,7 @@ task rqcfilter {
             removecat=t \
             removemouse=t \
             khist=t \
+            ~{filterbytile} \
             removemicrobes=t \
             sketch \
             kapa=t \

version.txt

@@ -1 +1 @@
-v1.0.24
+v1.0.25