Merge branch 'dev'

.gitignore

@@ -1,36 +1,49 @@
-# First, ignore everything
-*
-# Now, whitelist anything that's a directory
-!*/
+# ignore test results
 
+tests/test/*
 
-#keep everything in data
-!metadata/*
-results_pipeline/
-results_analysis
-resources/
-pipelines/pypiper
+# ignore built docs
+doc/build/*
 
-# And all the file types you're interested in.
-!*.sh
-!*.R
-!*.pl
-!*.py
-!*.c
-!*.md
-!*.sub
-!*readme.txt*
-!*README.txt*
-!*readme.md*
-!*README.md*
-!*.rst
+# generic ignore list:
 
-!*.xlsx
-!*.yaml
-!*.tsv
+# Compiled source 
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+*.pyc
+
+# Packages 
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases 
+*.log
+*.sql
+*.sqlite
+
+# OS generated files 
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
 
-#make sure to track .gitignore
-!.gitignore
+# Gedit temporary files 
+*~
 
-# ignore test results
-tests/test/*
+# libreoffice lock files:
+.~lock*

looper/looper.py

@@ -239,31 +239,33 @@ def run(prj, args, remaining_args):
 			# these arguments, then it should list looper_args=True and then we
 			# should add the arguments to the command string.
 
-			# Check for a pipeline config file
-			if hasattr(prj, "pipeline_config"):
-				# Index with 'pl_id' instead of 'pipeline' because we don't care about
-				# parameters here.
-				if hasattr(prj.pipeline_config, pl_id):
-					# First priority: pipeline config specified in project config
-					pl_config_file = getattr(prj.pipeline_config, pl_id)
-					if pl_config_file:  # make sure it's not null (which it could be provided as null)
-						if not os.path.isfile(pl_config_file):
-							print("Pipeline config file specified but not found: " + pl_config_file)
-							raise IOError(pl_config_file)
-						print("Found config file:" + getattr(prj.pipeline_config, pl_id))
-						# Append arg for config file if found
-						cmd += " -C " + pl_config_file
-
-			# Append output parent folder
-			cmd += " -O " + prj.metadata.results_subdir
-
-			# Append arg for cores (number of processors to use)
-			if submit_settings["cores"] > 1:
-				cmd += " -P " + submit_settings["cores"]
-
-			# Append arg for memory
-			if submit_settings["mem"] > 1:
-				cmd += " -M " + submit_settings["mem"]
+			if pipeline_interface.uses_looper_args(pl_id):
+
+				# Check for a pipeline config file
+				if hasattr(prj, "pipeline_config"):
+					# Index with 'pl_id' instead of 'pipeline' because we don't care about
+					# parameters here.
+					if hasattr(prj.pipeline_config, pl_id):
+						# First priority: pipeline config specified in project config
+						pl_config_file = getattr(prj.pipeline_config, pl_id)
+						if pl_config_file:  # make sure it's not null (which it could be provided as null)
+							if not os.path.isfile(pl_config_file):
+								print("Pipeline config file specified but not found: " + pl_config_file)
+								raise IOError(pl_config_file)
+							print("Found config file:" + getattr(prj.pipeline_config, pl_id))
+							# Append arg for config file if found
+							cmd += " -C " + pl_config_file
+
+				# Append output parent folder
+				cmd += " -O " + prj.metadata.results_subdir
+
+				# Append arg for cores (number of processors to use)
+				if submit_settings["cores"] > 1:
+					cmd += " -P " + submit_settings["cores"]
+
+				# Append arg for memory
+				if submit_settings["mem"] > 1:
+					cmd += " -M " + submit_settings["mem"]
 
 			# Add the command string and job name to the submit_settings object
 			submit_settings["JOBNAME"] = sample.sample_name + "_" + pipeline

looper/models.py

@@ -592,7 +592,7 @@ def check_sheet(self, dtype):
 		missing = [col for col in req if col not in self.df.columns]
 
 		if len(missing) != 0:
-			raise ValueError("Annotation sheet is missing columns: %s" % " ".join(missing))
+			raise ValueError("Annotation sheet (" + str(self.csv) + ") is missing columns: %s" % " ".join(missing))
 
 	def make_sample(self, series):
 		"""
@@ -1242,6 +1242,14 @@ def select_pipeline(self, pipeline_name):
 
 		return(self.looper_config[pipeline_name])
 
+	def uses_looper_args(self, pipeline_name):
+		config = self.select_pipeline(pipeline_name)
+
+		if hasattr(config, "looper_args") and config.looper_args:
+			return True
+		else:
+			return False
+
 	def get_pipeline_name(self, pipeline_name):
 		"""
 		:param pipeline_name: Name of pipeline.

tests/data/a.txt

@@ -0,0 +1 @@
+This is the content of test file a.

tests/data/b1.txt

@@ -0,0 +1 @@
+This is the content of test file b1.

tests/data/b2.txt

@@ -0,0 +1 @@
+This is the content of test file b2.

tests/data/b3.txt

@@ -0,0 +1 @@
+This is the content of test file b3.

tests/data/c.txt

@@ -0,0 +1 @@
+This is the content of test file c.

tests/merge.csv

@@ -0,0 +1,4 @@
+sample_name,file,file2,dcol1,col_modifier
+b,src1,src1,src1,1
+b,src1,src1,src1,2
+b,src1,src1,src1,3

tests/pipe_nolooperargs/config/pipeline_interface.yaml

@@ -0,0 +1,12 @@
+testpipeline.sh:
+  name: test_pipeline
+  looper_args: False
+  arguments:
+    "--input": file
+  resources:
+    default:
+      file_size: "0"
+      cores: "8"
+      mem: "32000"
+      time: "2-00:00:00"
+      partition: "longq"

tests/pipe_nolooperargs/config/protocol_mappings.yaml

@@ -0,0 +1,2 @@
+testlib: testpipeline.sh
+testngs: testngs.sh

tests/pipe_nolooperargs/pipelines/testngs.sh

@@ -0,0 +1,3 @@
+#!/bin/bash 
+
+echo $@

tests/pipe_nolooperargs/pipelines/testpipeline.sh

@@ -0,0 +1,3 @@
+#!/bin/bash 
+
+echo $@

tests/samples.csv

@@ -0,0 +1,5 @@
+sample_name,library,file,file2,organism,nonmerged_col,data_source,dcol2
+a,testlib,src3,src3,,src3,src3,
+b,testlib,,,,src3,src3,src1
+c,testlib,src3,src3,,src3,src3,
+d,testngs,src2,src3,human,,src3,