From 728f268bbadfc03260ea99c4d2b4879503ca44d8 Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Wed, 7 Feb 2024 10:46:03 -0500
Subject: [PATCH] Patch: Use tmpdir/lscratch with fastqc due to gpfs issue.

---
 VERSION             |  2 +-
 config/cluster.json |  6 ++++--
 workflow/Snakefile  | 44 ++++++++++++++++++++++++++++++++++++++++++--
 3 files changed, 47 insertions(+), 5 deletions(-)

diff --git a/VERSION b/VERSION
index b49b253..d3532a1 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.5.6
+0.5.7
diff --git a/config/cluster.json b/config/cluster.json
index 7a0a2cd..01f4040 100644
--- a/config/cluster.json
+++ b/config/cluster.json
@@ -48,12 +48,14 @@
         "mem": "24g"
     },
     "rawfastqc": {
-        "threads": "8"
+        "threads": "8",
+        "gres": "lscratch:64"
     },
     "fastqc": {
         "mem": "24g",
         "threads": "32",
-        "time": "18:00:00"
+        "time": "18:00:00",
+        "gres": "lscratch:64"
     },
     "fastq_screen": {
         "mem": "24g",
diff --git a/workflow/Snakefile b/workflow/Snakefile
index c9d16d0..c50388f 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -693,16 +693,36 @@ rule rawfastqc:
     params:
         rname='rawfastqc',
         outdir=join(workpath,"rawfastQC"),
+        tmpdir=tmpdir,
     envmodules: 
         config['tools']['FASTQCVER']
     threads:
         int(allocated("threads", "rawfastqc", cluster))
     shell: """
+    # Setups temporary directory for
+    # intermediate files with built-in 
+    # mechanism for deletion on exit
+    if [ ! -d "{params.tmpdir}" ]; then mkdir -p "{params.tmpdir}"; fi
+    tmp=$(mktemp -d -p "{params.tmpdir}")
+    trap 'rm -rf "${{tmp}}"' EXIT
+
+    # Running fastqc with local
+    # disk or a tmpdir, fastqc
+    # has been observed to lock
+    # up gpfs filesystems, adding
+    # this on request by HPC staff
     fastqc \\
         {input.R1} \\
         {input.R2} \\
         -t {threads} \\
-        -o {params.outdir}
+        -o "${{tmp}}"
+
+    # Copy output files from tmpdir
+    # to output directory
+    find "${{tmp}}" \\
+        -type f \\
+        \\( -name '*.html' -o -name '*.zip' \\) \\
+        -exec cp {{}} {params.outdir} \\;
     """
 
 
@@ -725,16 +745,36 @@ rule fastqc:
     params:
         rname='fastqc',
         outdir=join(workpath,"fastQC"),
+        tmpdir=tmpdir,
     envmodules: 
         config['tools']['FASTQCVER']
     threads:
         int(allocated("threads", "fastqc", cluster))
     shell: """
+    # Setups temporary directory for
+    # intermediate files with built-in 
+    # mechanism for deletion on exit
+    if [ ! -d "{params.tmpdir}" ]; then mkdir -p "{params.tmpdir}"; fi
+    tmp=$(mktemp -d -p "{params.tmpdir}")
+    trap 'rm -rf "${{tmp}}"' EXIT
+
+    # Running fastqc with local
+    # disk or a tmpdir, fastqc
+    # has been observed to lock
+    # up gpfs filesystems, adding
+    # this on request by HPC staff
     fastqc \\
         {input.R1} \\
         {input.R2} \\
         -t {threads} \\
-        -o {params.outdir}
+        -o "${{tmp}}"
+    
+    # Copy output files from tmpdir
+    # to output directory
+    find "${{tmp}}" \\
+        -type f \\
+        \\( -name '*.html' -o -name '*.zip' \\) \\
+        -exec cp {{}} {params.outdir} \\;
     """