From 64cd0713448d942ed5dca303d822f1505900ec77 Mon Sep 17 00:00:00 2001
From: Kaitlyn Jiayi Li <kli@lanl.gov>
Date: Thu, 27 Jun 2024 13:27:46 -0700
Subject: [PATCH 1/3] added extend=f

---
 rqcfilter.wdl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/rqcfilter.wdl b/rqcfilter.wdl
index 31df6e1..37d6136 100644
--- a/rqcfilter.wdl
+++ b/rqcfilter.wdl
@@ -174,6 +174,7 @@ task rqcfilter{
             barcodefilter=f \
             chastityfilter=f \
             clumpify=t \
+            extend=f \
             in=~{input_fastq} \
             jni=t \
             khist=t \

From 24e8b810db7b9f43d5350c7a3f003d1a8abd19e8 Mon Sep 17 00:00:00 2001
From: Kaitlyn Jiayi Li <kli@lanl.gov>
Date: Thu, 27 Jun 2024 14:41:59 -0700
Subject: [PATCH 2/3] working on makeinfo spacing

---
 rqcfilter.wdl | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/rqcfilter.wdl b/rqcfilter.wdl
index 37d6136..973a18e 100644
--- a/rqcfilter.wdl
+++ b/rqcfilter.wdl
@@ -171,12 +171,15 @@ task rqcfilter{
         fi
         
         rqcfilter2.sh \
+            in=~{input_fastq} \
+            rqcfilterdata=~{if gcloud_env then gcloud_db_path else rqcfilterdata} \
+            path=filtered \
             barcodefilter=f \
             chastityfilter=f \
             clumpify=t \
             extend=f \
-            in=~{input_fastq} \
             jni=t \
+            usejni=f \
             khist=t \
             log=status.log \
             maq=10 \
@@ -185,7 +188,6 @@ task rqcfilter{
             mlf=0.33 \
             mtst=t \
             outribo=ribo.fq.gz \
-            path=filtered \
             phix=t \
             pigz=t \
             qtrim=r \
@@ -196,16 +198,14 @@ task rqcfilter{
             removemouse=t \
             removeribo=t \
             rna=t \
-            rqcfilterdata=~{if gcloud_env then gcloud_db_path else rqcfilterdata} \
             sketch=t \
             stats=~{filename_stat} \
             trimfragadapter=t \
             trimpolyg=5 \
             trimq=0 \
             unpigz=t \
-            usejni=f \
-            ~{if (defined(memory)) then "-Xmx" + memory else "-Xmx101077m" } \
-            ~{if (defined(threads)) then "threads=" + threads else "threads=auto" } \
+            ~{if (defined(memory)) then "-Xmx" + memory + " " else "-Xmx101077m " } \
+            ~{if (defined(threads)) then "threads=" + threads + " " else "threads=auto " } \
             > >(tee -a  ~{filename_outlog}) \
             2> >(tee -a ~{filename_errlog}  >&2)
 

From d4e056253a2aae0f0df6ae2ea0d76e1752ab4263 Mon Sep 17 00:00:00 2001
From: Kaitlyn Jiayi Li <kli@lanl.gov>
Date: Mon, 1 Jul 2024 16:13:53 -0700
Subject: [PATCH 3/3] fixed memory issues

---
 rqcfilter.wdl | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/rqcfilter.wdl b/rqcfilter.wdl
index 973a18e..4642155 100644
--- a/rqcfilter.wdl
+++ b/rqcfilter.wdl
@@ -10,7 +10,7 @@ workflow metaTReadsQC {
         Boolean gcloud_env=false
         Array[String] input_files
         String  database="/refdata/"
-        String  rqc_mem = "200G"
+        String  rqc_mem = "115G"
         Int     rqc_thr = 64
         String  interleave_mem = "10G"
     }
@@ -171,9 +171,6 @@ task rqcfilter{
         fi
         
         rqcfilter2.sh \
-            in=~{input_fastq} \
-            rqcfilterdata=~{if gcloud_env then gcloud_db_path else rqcfilterdata} \
-            path=filtered \
             barcodefilter=f \
             chastityfilter=f \
             clumpify=t \
@@ -188,6 +185,7 @@ task rqcfilter{
             mlf=0.33 \
             mtst=t \
             outribo=ribo.fq.gz \
+            path=filtered \
             phix=t \
             pigz=t \
             qtrim=r \
@@ -198,17 +196,21 @@ task rqcfilter{
             removemouse=t \
             removeribo=t \
             rna=t \
+            rqcfilterdata=~{if gcloud_env then gcloud_db_path else rqcfilterdata} \
             sketch=t \
             stats=~{filename_stat} \
             trimfragadapter=t \
             trimpolyg=5 \
             trimq=0 \
             unpigz=t \
-            ~{if (defined(memory)) then "-Xmx" + memory + " " else "-Xmx101077m " } \
-            ~{if (defined(threads)) then "threads=" + threads + " " else "threads=auto " } \
+            ~{if (defined(memory)) then "-Xmx" + memory else "-Xmx101077m" } \
+            ~{if (defined(threads)) then "threads=" + threads else "threads=auto" } \
+            in=~{input_fastq} \
             > >(tee -a  ~{filename_outlog}) \
             2> >(tee -a ~{filename_errlog}  >&2)
 
+            # moved input file to end for processing of resubmit.sh line, the rest is kinda alphabetized 
+
         python <<CODE
         import json
         f = open("~{filename_stat}",'r')
@@ -234,7 +236,7 @@ task rqcfilter{
      }
      runtime {
         docker: container
-        memory: "210 GiB"
+        memory: "140 GiB"
         cpu:  32
     }
 }
@@ -249,10 +251,11 @@ task make_info_file {
     command<<<
         set -oeu pipefail
         sed -n 2,5p ~{info_file} 2>&1 | \
-          perl -ne 's:in=/.*/(.*) :in=$1:; s/#//; s/BBTools/BBTools(1)/; print;' > \
+          sed -e 's/^#//; s/in=[^ ]*/in=filename.fastq.gz/; s/#//g; s/BBTools/BBTools(1)/g;' > \
          ~{prefix}_readsQC.info
         echo -e "\n(1) B. Bushnell: BBTools software package, http://bbtools.jgi.doe.gov/" >> \
          ~{prefix}_readsQC.info
+         # perl -ne 's:in=/.*/(.*) :in=$1:; s/#//; s/BBTools/BBTools(1)/; print;' > \ # for container microbiomedata/workflowmeta:1.1.1
     >>>
 
     output {