Add in tmp directory.

workflow/conf/install_R_packages.R

+install.packages("snow", repos="http://cran.us.r-project.org")
+install.packages("snowfall", repos="http://cran.us.r-project.org")
+install.packages("bitops", repos="http://cran.us.r-project.org")
+install.packages("caTools", repos="http://cran.us.r-project.org")
+source("http://bioconductor.org/biocLite.R")
+biocLite("Rsamtools",suppressUpdates=TRUE)
+install.packages("../../phantompeakqualtools/spp_1.14.tar.gz")

workflow/scripts/map_qc.py

@@ -158,8 +158,8 @@ def dedup_mapped(bam, bam_basename, paired):
                     " --overflow-list-size=20000000 --io-buffer-size=256"
     with open(dup_file_qc_filename, 'w') as fh:
         sambamba_markdup_command = (
-            "sambamba markdup -t %d %s %s %s"
-            % (cpu_count(), sambamba_params, bam, tmp_dup_mark_filename)
+            "sambamba markdup -t %d %s --tmpdir=%s %s %s"
+            % (cpu_count(), sambamba_params, os.getcwd(), bam, tmp_dup_mark_filename)
             )
         logger.info(sambamba_markdup_command)
         subprocess.check_call(