remove eager log from output and command

ktmeaton · Apr 27, 2021 · 62c1c5c · 62c1c5c
1 parent 3790bdd
commit 62c1c5c
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/workflow/rules/alignment.smk b/workflow/rules/alignment.smk
@@ -21,7 +21,7 @@ rule eager:
         final_bam = results_dir + "/eager/{reads_origin}/{sample}/final_bams/{sample}.bam",
         eager_tsv = results_dir + "/eager/{reads_origin}/{sample}/metadata_{sample}.tsv",
         log_html  = results_dir + "/eager/{reads_origin}/{sample}/{sample}.html",
-        log_txt  = results_dir + "/eager/{reads_origin}/{sample}/{sample}.log",
+        #log_txt  = results_dir + "/eager/{reads_origin}/{sample}/{sample}.log",
     wildcard_constraints:
         reads_origin = "(sra|local)",
     resources:
@@ -58,7 +58,7 @@ rule eager:
             --max_memory {resources.mem_mb}.MB \
             --max_time {resources.time_min}m \
 			{config[eager_other]} \
-            -resume > {output.log_txt};
+            -resume;
         {scripts_dir}/eager_cleanup.sh {results_dir} {wildcards.reads_origin} {wildcards.sample};
         """
 

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -22,8 +22,11 @@ rule qualimap:
 	cpus=workflow.global_resources["cpus"] if ("cpus" in workflow.global_resources) else 1,
         mem_mb=workflow.global_resources["mem_mb"] if ("mem_mb" in workflow.global_resources) else 4000,
     shell:
-        "samtools view -b -q {config[snippy_map_qual]} {input.snippy_dir}/{wildcards.sample}.bam > {output.bamq}; "
-        "qualimap bamqc -bam {output.bamq} --skip-duplicated -c -outformat 'HTML' -outdir {output.dir} -nt {resources.cpus} 1> {output.log}; "
+        """
+        export JAVA_OPTS='-Djava.awt.headless=true';
+        samtools view -b -q {config[snippy_map_qual]} {input.snippy_dir}/{wildcards.sample}.bam > {output.bamq};
+        qualimap bamqc -bam {output.bamq} --skip-duplicated -c -outformat 'HTML' -outdir {output.dir} -nt {resources.cpus} 1> {output.log};
+        """
 
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