Merge branch 'main' of github.com:snakemake/snakemake

.github/workflows/main.yml

@@ -57,7 +57,9 @@ jobs:
           conda install -c conda-forge -q mamba
           mamba env create -q --name snakemake --file test-environment.yml
           # additionally add singularity
-          mamba install -c conda-forge -n snakemake singularity
+          # TODO remove version constraint: needed because 3.8.7 fails with missing libz:
+          # bin/unsquashfs: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
+          mamba install -c conda-forge -n snakemake "singularity<=3.8.6"
       
       - name: Setup apt dependencies
         run: |

misc/vim/syntax/snakemake.vim

@@ -47,8 +47,10 @@ source $VIMRUNTIME/indent/python.vim
 syn keyword pythonStatement include workdir onsuccess onerror onstart
 syn keyword pythonStatement ruleorder localrules configfile group 
 syn keyword pythonStatement wrapper conda shadow
-syn keyword pythonStatement input output params wildcards priority message threads resources singularity wildcard_constraints
+syn keyword pythonStatement input output params wildcards priority message
+syn keyword pythonStatement threads resources singularity container wildcard_constraints
 syn keyword pythonStatement version run shell benchmark snakefile log script
+syn keyword pythonStatement default_target template_engine
 syn keyword pythonStatement rule subworkflow checkpoint nextgroup=pythonFunction skipwhite
 syn keyword pythonBuiltinObj config checkpoints rules
 syn keyword pythonBuiltinFunc directory ancient pipe unpack expand temp touch protected

snakemake/dag.py

@@ -1308,6 +1308,12 @@ def handle_pipes_and_services(self):
                             "a dead lock.".format(f),
                             rule=job.rule,
                         )
+                    elif is_pipe and depending[0].is_norun:
+                        raise WorkflowError(
+                            f"Output file {f} is marked as pipe but is requested by a rule that "
+                            "does not execute anything. This is not allowed because it would lead "
+                            "to a dead lock."
+                        )
 
                     for dep in depending:
                         if dep.is_run:

snakemake/deployment/conda.py

@@ -564,7 +564,9 @@ def __init__(self, container_img=None, prefix_path=None):
 
             if prefix_path is None or container_img is not None:
                 self.prefix_path = json.loads(
-                    shell.check_output(self._get_cmd("conda info --json"))
+                    shell.check_output(
+                        self._get_cmd("conda info --json"), universal_newlines=True
+                    )
                 )["conda_prefix"]
             else:
                 self.prefix_path = prefix_path

snakemake/workflow.py

@@ -392,7 +392,8 @@ def norm_rule_relpath(f, rule):
                 )
             else:
                 raise WorkflowError(
-                    "Error executing git:\n{}".format(e.stderr.decode())
+                    "Error executing git (Snakemake requires git to be installed for "
+                    "remote execution without shared filesystem):\n" + e.stderr.decode()
                 )
 
         return files

tests/test_pipe_depend/Snakefile

@@ -0,0 +1,11 @@
+rule all:
+    input:
+        "test.txt"
+
+
+rule a:
+    output:
+        pipe("test.txt")
+    shell:
+        "echo test > {output}"
+

tests/tests.py

@@ -1565,3 +1565,13 @@ def test_service_jobs():
 
 def test_incomplete_params():
     run(dpath("test_incomplete_params"), dryrun=True, printshellcmds=True)
+
+
+@skip_on_windows  # no pipe support on windows
+def test_pipe_depend():
+    run(dpath("test_pipe_depend"), shouldfail=True)
+
+
+@skip_on_windows  # no pipe support on windows
+def test_pipe_depend_target_file():
+    run(dpath("test_pipe_depend"), targets=["test.txt"], shouldfail=True)