fix: correct some parameters of ppqt tagalign and ppqt

OpenOmics · Jan 3, 2025 · ddbafc9 · ddbafc9
1 parent 5d05803
commit ddbafc9
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Showing 2 changed files with 20 additions and 15 deletions.
diff --git a/workflow/rules/paired/trim_align_dedup.smk b/workflow/rules/paired/trim_align_dedup.smk
@@ -260,19 +260,26 @@ rule ppqt:
         tmpdir                              = tmpdir,
     container: 
         config['images']['ppqt']
+    threads:
+        int(cluster['ppqt'].get('threads', cluster['__default__']['threads']))
     shell: 
         """
         if [ ! -d "{params.tmpdir}" ]; then mkdir -p "{params.tmpdir}"; fi
         tmp=$(mktemp -d -p "{params.tmpdir}")
         trap 'rm -rf "${{tmp}}"' EXIT
 
         samtools view -b \\
+            -@ {threads} \\
             -f 66 \\
             -o ${{tmp}}/bam1.f66.bam {input};
         samtools index ${{tmp}}/bam1.f66.bam;
-        run_spp.R -c=${{tmp}}/bam1.f66.bam \
-                    -savp={output.pdf} -out={output.ppqt} \
-                    -tmpdir=${{tmp}} -rf
+        run_spp.R \\
+            -c=${{tmp}}/bam1.f66.bam \\
+            -savp={output.pdf} \\
+            -out={output.ppqt} \\
+            -tmpdir=${{tmp}} \\
+            -p={threads} \\
+            -rf
 
         python {params.scriptPy} -i {output.ppqt} -o {output.txt}
         """

diff --git a/workflow/rules/single/trim_align_dedup.smk b/workflow/rules/single/trim_align_dedup.smk
@@ -232,7 +232,7 @@ rule ppqt:
     container: 
         config['images']['ppqt']
     threads:
-        cluster['ppqt'].get('threads', cluster['__default__']['threads'])
+        int(cluster['ppqt'].get('threads', cluster['__default__']['threads']))
     shell: 
         """
         if [ ! -d "{params.tmpdir}" ]; then mkdir -p "{params.tmpdir}"; fi
@@ -243,14 +243,14 @@ rule ppqt:
             -c={input.bam} \\
             -savp={output.pdf} \\
             -out={output.ppqt} \\
-            -p={threads} \\
-            -tmpdir=${{tmp}} 
+            -tmpdir=${{tmp}} \\
+            -p={threads}
         """
 
 
 rule ppqt_tagalign:
     input:
-        bam                                 = join(bam_dir, "{name}.Q5DD_tagAlign.gz")
+        tagalign                            = join(bam_dir, "{name}.Q5DD_tagAlign.gz")
     output:                                          
         ppqt                                = join(ppqt_dir, "{name}.Q5DD_tagAlign.ppqt.txt"),
         pdf                                 = join(ppqt_dir, "{name}.Q5DD_tagAlign.pdf"),
@@ -262,23 +262,21 @@ rule ppqt_tagalign:
         tmpdir                              = tmpdir,
     container: 
         config['images']['ppqt']
-        # "docker://seqeralabs/phantompeakqualtools:latest"
     threads:
-        cluster['ppqt_tagalign'].get('threads', cluster['__default__']['threads'])
+        int(cluster['ppqt_tagalign'].get('threads', cluster['__default__']['threads']))
     shell: 
         """
         if [ ! -d "{params.tmpdir}" ]; then mkdir -p "{params.tmpdir}"; fi
         tmp=$(mktemp -d -p "{params.tmpdir}")
         trap 'rm -rf "${{tmp}}"' EXIT
-
-        ln -s {input.bam} ${{tmp}}/{wildcards.name}.Q5DD_tagAlign.gz
-        zcat ${{tmp}}/{wildcards.name}.Q5DD_tagAlign.gz | head
+        # ppqt will not work unless file name ends with ".tagAlign"
+        # "Q5DD_tagAlign" will not work
+        gunzip -C {input.tagalign} > ${{tmp}}/{wildcards.name}.Q5DD.tagAlign
         run_spp.R \\
-            -c=${{tmp}}/{wildcards.name}.Q5DD_tagAlign.gz \\
+            -c=${{tmp}}/{wildcards.name}.Q5DD.tagAlign \\
             -savp={output.pdf} \\
             -out={output.ppqt} \\
-            -p={threads} \\
-            -tmpdir=${{tmp}}
+            -p={threads} 
         """