From 39e5ae65740d65181e718ccae2023104cf797b9a Mon Sep 17 00:00:00 2001
From: Kaitlyn Jiayi Li <kli@lanl.gov>
Date: Thu, 25 Jul 2024 13:28:04 -0700
Subject: [PATCH] added ribosomal output

---
 .github/workflows/wdl_linter.yml | 28 ++++++++++++++++++++++++++++
 rqcfilter.wdl                    | 11 +++++++++--
 version.txt                      |  2 +-
 3 files changed, 38 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/wdl_linter.yml

diff --git a/.github/workflows/wdl_linter.yml b/.github/workflows/wdl_linter.yml
new file mode 100644
index 0000000..18381f3
--- /dev/null
+++ b/.github/workflows/wdl_linter.yml
@@ -0,0 +1,28 @@
+name: MiniWDL linter CI
+
+on:
+  pull_request:
+    branches: main
+
+jobs:
+  run-miniwdl:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8' # specify the Python version you need
+
+    - name: Install MiniWDL
+      run: |
+        python -m pip install --upgrade pip
+        pip install miniwdl
+
+    - name: Run MiniWDL
+      run: |
+        # Add the commands to run your MiniWDL workflow
+        miniwdl check --suppress UnknownRuntimeKey rqcfilter.wdl
\ No newline at end of file
diff --git a/rqcfilter.wdl b/rqcfilter.wdl
index 04caa03..5b02114 100644
--- a/rqcfilter.wdl
+++ b/rqcfilter.wdl
@@ -55,13 +55,15 @@ workflow metaTReadsQC {
             prefix = prefix,
             filtered = qc.filtered,
             filtered_stats = qc.stat,
-            filtered_stats2 = qc.stat2
+            filtered_stats2 = qc.stat2,
+            filtered_ribo = qc.filtered_ribo
     }
     output {
         File filtered_final = finish_rqc.filtered_final
         File filtered_stats_final = finish_rqc.filtered_stats_final
         File filtered_stats2_final = finish_rqc.filtered_stats2_final
         File rqc_info = make_info_file.rqc_info
+        File filtered_ribo_final = finish_rqc.filtered_ribo_final
     }
 }
 
@@ -158,6 +160,7 @@ task rqcfilter{
         String filename_stat2="filtered/filterStats2.txt"
         String filename_stat_json="filtered/filterStats.json"
         String filename_reproduce="filtered/reproduce.sh"
+        String filename_ribo = "filtered/rRNA.fastq.gz"
     }
 
      command<<<
@@ -186,7 +189,7 @@ task rqcfilter{
             minlen=51 \
             mlf=0.33 \
             mtst=t \
-            outribo=ribo.fq.gz \
+            outribo=rRNA.fastq.gz \
             path=filtered \
             phix=t \
             pigz=t \
@@ -234,6 +237,7 @@ task rqcfilter{
             File stat2 = filename_stat2
             File info_file = filename_reproduce
             File filtered = glob("filtered/*fastq.gz")[0]
+            File filtered_ribo = filename_ribo
             File json_out = filename_stat_json
      }
      runtime {
@@ -276,6 +280,7 @@ task finish_rqc {
         File   filtered_stats
         File   filtered_stats2
         File   filtered
+        File   filtered_ribo
         String container
         String prefix
     }
@@ -288,6 +293,7 @@ task finish_rqc {
         ln ~{filtered} ~{prefix}_filtered.fastq.gz || ln -s ~{filtered} ~{prefix}_filtered.fastq.gz
         ln ~{filtered_stats} ~{prefix}_filterStats.txt || ln -s ~{filtered_stats} ~{prefix}_filterStats.txt
         ln ~{filtered_stats2} ~{prefix}_filterStats2.txt || ln -s ~{filtered_stats2} ~{prefix}_filterStats2.txt
+        ln ~{filtered_ribo} ~{prefix}_rRNA.fastq.gz || ln -s ~{filtered_ribo} ~{prefix}_rRNA.fastq.gz
 
        # Generate stats but rename some fields untilt the script is fixed.
        /scripts/rqcstats.py ~{filtered_stats} > stats.json
@@ -298,6 +304,7 @@ task finish_rqc {
         File filtered_final = "~{prefix}_filtered.fastq.gz"
         File filtered_stats_final = "~{prefix}_filterStats.txt"
         File filtered_stats2_final = "~{prefix}_filterStats2.txt"
+        File filtered_ribo_final = "~{prefix}_rRNA.fastq.gz"
     }
 
     runtime {
diff --git a/version.txt b/version.txt
index f9cece5..7df503e 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-v0.0.3
+v0.0.4