fix: dependency issue in job files

meono · Sep 12, 2016 · 7945d4e · 7945d4e
1 parent 8cb2118
commit 7945d4e
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/TODO b/TODO
@@ -5,4 +5,8 @@
 - get proper reads for testing under example_notebooks/reads/raw
 - get value for project number in job scripts
 - make hisat indexes for all the available genomes
-- define a quality score threshold and use it to block or continue RNAseq (in master_qsub)
+- define a quality score threshold and use it to block or continue RNAseq (in master_qsub)
+
+- Defining replicates of a sample fails under specific circumstances:
+    -- If the names are too simlar: MG1655-a, b, c and MG1655-1, 2, 3 would be grouped under the same sample with 6 replicates.
+    -- If the only difference in groups is the sample ID: reads from MG1655-a_S11, MG1655-a_S12, MG1655-a_S13 would be considered under one replicate.
diff --git a/iLoop_RNAseq_pipeline/master_qsub.py b/iLoop_RNAseq_pipeline/master_qsub.py
@@ -306,7 +306,7 @@ def quant_jobs(project_path, sample, mergejob, ref, defaults, ppn='8', walltime=
     jobstr += [job_header.replace('JOBNAME', '_'.join([sample] + ['cuffquant']))
                    .replace('WALLTIME', walltime)
                    .replace('PROJECT', defaults['project'])
-                   .replace('DEPEND', 'afterok:{}'.format(mergejob))
+                   .replace('DEPEND', ('afterok:{}'.format(mergejob) if mergejob != '' else ''))
                    .replace('JOB_OUTPUTS', abspath(join_path(project_path, 'job_outputs')))
                    .replace('EMAILADDRESS', defaults['email'])]