Merge pull request #99 from sanjaynagi/add-logs-coverage

coverage was not saving logs to file
sanjaynagi · Jun 18, 2024 · d94e12f · d94e12f
2 parents 4de4ffb + 68c5ff1
commit d94e12f
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/workflow/rules/alignment.smk b/workflow/rules/alignment.smk
@@ -35,6 +35,7 @@ rule KallistoQuant:
     wrapper:
         "v1.15.0/bio/kallisto/quant"
 
+
 rule GenomeUnzip:
     """
     Index the reference genome with samtools
@@ -48,6 +49,7 @@ rule GenomeUnzip:
     shell:
         "gzip -d -c {input} > {output} 2> {log}"
 
+
 rule GenomeIndex:
     """
     Index the reference genome with samtools

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -51,7 +51,7 @@ rule BamStats:
     log:
         "logs/BamStats/{sample}.log",
     wrapper:
-        "v1.15.0/bio/samtools/flagstat"
+        "v3.12.1/bio/samtools/flagstat"
 
 
 rule Coverage:
@@ -71,7 +71,7 @@ rule Coverage:
         prefix=lambda w, output: output[0].split(os.extsep)[0],
     threads: 8
     shell:
-        "mosdepth --threads {threads} --fast-mode {params.prefix} {input.bam}"
+        "mosdepth --threads {threads} --fast-mode {params.prefix} {input.bam} 2> {log}"
 
 
 rule vcfStats: