Fixed now outdated --no-dedup arg in wafergen tests. Fixed accidental…

…ly skipped module tests in pipeline

rnaseq/wafergen-scrna/tests.sh

@@ -103,9 +103,9 @@ if [ $skip_real_runs -ne 1 ]; then
     jid=$(tail -n 1 $odir/logs/submission.log  | cut -f 3 -d ' ')
     echo "Started job $jid writing to $odir. You will receive an email"
 
-    echo "Realrun no_dedup" | tee -a $log
+    echo "Realrun dedup" | tee -a $log
     odir=$($DOWNSTREAM_OUTDIR_PY -r $(whoami) -p $PIPELINE)
-    eval $cmd_base --no-dedup -o $odir -v >> $log 2>&1
+    eval $cmd_base --dedup -o $odir -v >> $log 2>&1
     # magically works even if line just contains id as in the case of pbspro
     jid=$(tail -n 1 $odir/logs/submission.log  | cut -f 3 -d ' ')
     echo "Started job $jid writing to $odir. You will receive an email"

tools/pipelint.py

@@ -111,6 +111,7 @@ def check_modules(pipeline_dir):
 
     is_ok = True
     module_cfgs = glob.glob(os.path.join(pipeline_dir, "cfg/modules.yaml"))
+    assert len(module_cfgs) > 0
     modules = dict()
     for cfg in module_cfgs:
         with open(cfg) as fh:
@@ -139,7 +140,14 @@ def main(pipelinedirs,
     logger.warning("include other existing tools here: check_cluster_conf.py...")
 
     snakefiles = [os.path.join(d, "Snakefile") for d in pipelinedirs]
-
+
+    if not no_modules_check:
+        for d in pipelinedirs:
+            if not check_modules(d):
+                print("FAILED: Modules check for {}".format(d))
+            else:
+                print("OK: Modules check for {}".format(d))
+
     includes = []
     for f in snakefiles:
         assert os.path.exists(f)
@@ -148,12 +156,6 @@ def main(pipelinedirs,
         else:
             print("OK: Expected files for {}".format(f))
 
-        if not no_modules_check:
-            if not check_modules(f):
-                print("FAILED: Modules check for {}".format(f))
-            else:
-                print("OK: Modules check for {}".format(f))
-
         includes.extend(get_includes_from_snakefile(f))