Adding bowtie/1.X log to multiqc input

OpenOmics · Jul 7, 2023 · 7a3c8e6 · 7a3c8e6
1 parent dc41c01
commit 7a3c8e6
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Showing 2 changed files with 17 additions and 0 deletions.
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
@@ -15,16 +15,29 @@ rule mirdeep2_mapper:
     output:
         arf       = join(workpath, "mirdeep2", "mapper", "{sample}_mapped.arf"),
         collapsed = join(workpath, "mirdeep2", "mapper", "{sample}_collapsed.fa"),
+        new_log   = join(workpath, "mirdeep2", "mapper", "{sample}", "{sample}.bowtie.log"),
     params:
         rname = "mapper",
         # Minimum read length also
         # used for trimming reads
         min_len = min_read_length,
         bw_index = config['references'][genome]['bowtie1_index'],
+        tmpdir   = join(workpath, "mirdeep2", "mapper", "{sample}"),
     envmodules: config['tools']['bowtie'],
     container: config['images']['mir-seek'],
     threads: int(allocated("threads", "mirdeep2_mapper", cluster)),
     shell: """
+    # Setups temporary directory for
+    # intermediate files, miRDeep2
+    # output directories rely on
+    # timestamps, this helps avoid
+    # collision due to multiple runs
+    # of the same sample, needed for
+    # the bowtie/1.X log files
+    if [ ! -d "{params.tmpdir}" ]; then mkdir -p "{params.tmpdir}"; fi
+    tmp=$(mktemp -d -p "{params.tmpdir}")
+    cd "${{tmp}}"
+
     # Aligns reads to the reference 
     # genome with Bowtie/1.X, allows
     # one mismatch in the alignment
@@ -41,4 +54,7 @@ rule mirdeep2_mapper:
         -t {output.arf} \\
         -v \\
         -o {threads}
+    
+    # Rename bowtie/1.X log file
+    mv "${{tmp}}/bowtie.log" "{output.new_log}"
     """
diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -74,6 +74,7 @@ rule multiqc:
         expand(join(workpath, "fastqc", "{sample}.R1_fastqc.zip"), sample=samples),
         expand(join(workpath, "fastqc", "{sample}_trimmed_fastqc.zip"), sample=samples),
         expand(join(workpath, "mirdeep2", "mapper", "{sample}_mapped.arf"), sample=samples),
+        expand(join(workpath, "mirdeep2", "mapper", "{sample}", "{sample}.bowtie.log"), sample=samples),
     output:
         html = join(workpath, "reports", "multiqc_report.html"),
     params: