diff --git a/edalize/apicula.py b/edalize/apicula.py
index b7fe54e7b..b2b4bae92 100644
--- a/edalize/apicula.py
+++ b/edalize/apicula.py
@@ -62,7 +62,7 @@ def configure_main(self):
         depends = self.name+'.pack'
         targets = self.name+'.fs'
         command = ['gowin_pack', '-d', self.tool_options.get('device'), '-o', targets, depends]
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         commands.set_default_target(targets)
         commands.write(os.path.join(self.work_root, 'Makefile'))
diff --git a/edalize/edatool.py b/edalize/edatool.py
index 85fe5f6ee..bb09c60ba 100644
--- a/edalize/edatool.py
+++ b/edalize/edatool.py
@@ -236,6 +236,14 @@ def __init__(self, command, targets, depends):
                 self.targets = targets
                 self.depends = depends
 
+        class Target:
+            def __init__(self, target, phony=False):
+                self.target = target
+                self.phony = phony
+
+            def __str__(self):
+                return str(self.target)
+
         def __init__(self):
             self.commands = []
             self.header = "#Auto generated by Edalize\n\n"
@@ -254,14 +262,22 @@ def write(self, outfile):
 
                 f.write(f"all: {self.default_target}\n")
 
+                phony_targets = ["all"]
                 for c in self.commands:
-                    f.write(f"\n{' '.join(c.targets)}:")
+                    cmd_targets = []
+                    for t in c.targets:
+                        cmd_targets.append(str(t))
+                        if t.phony:
+                            phony_targets.append(str(t))
+                    f.write(f"\n{' '.join(cmd_targets)}:")
                     for d in c.depends:
-                        f.write(" "+d)
+                        f.write(" "+str(d))
                     f.write("\n")
 
-                    if c.command:
-                        f.write(f"\t$(EDALIZE_LAUNCHER) {' '.join(c.command)}\n")
+                    for cmd in c.command:
+                        f.write(f"\t$(EDALIZE_LAUNCHER) {' '.join(cmd)}\n")
+
+                f.write(f"\n.PHONY: {' '.join(phony_targets)}\n")
 
     def set_default_target(self, target):
         self.default_target = target
diff --git a/edalize/icestorm.py b/edalize/icestorm.py
index ad6e9ce4e..0cce6790a 100644
--- a/edalize/icestorm.py
+++ b/edalize/icestorm.py
@@ -67,7 +67,7 @@ def configure_main(self):
             command = ['arachne-pnr']
             command += self.tool_options.get('arachne_pnr_options', [])
             command += ['-p', depends, '-o', targets]
-            commands.add(command, [depends], [targets])
+            commands.add([command], [self.EdaCommands.Target(depends)], [targets])
             set_default_target(self.name+'.bin')
         elif pnr == 'next':
             nextpnr = Nextpnr(yosys.edam, self.work_root)
@@ -82,20 +82,20 @@ def configure_main(self):
         depends = self.name+'.asc'
         targets = self.name+'.bin'
         command = ['icepack', depends, targets]
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         #Timing analysis
         depends = self.name+'.asc'
         targets = self.name+'.tim'
         command = ['icetime', '-tmd', part or '', depends, targets]
-        commands.add(command, [targets], [depends])
-        commands.add([], ["timing"], [targets])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
+        commands.add([], [self.EdaCommands.Target("timing", phony=True)], [targets])
 
         #Statistics
         depends = self.name+'.asc'
         targets = self.name+'.stat'
         command = ['icebox_stat', depends, targets]
-        commands.add(command, [targets], [depends])
-        commands.add([], ["stats"], [targets])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
+        commands.add([], [self.EdaCommands.Target("stats", phony=True)], [targets])
 
         commands.write(os.path.join(self.work_root, 'Makefile'))
diff --git a/edalize/nextpnr.py b/edalize/nextpnr.py
index cdfa35366..3b09b7db8 100644
--- a/edalize/nextpnr.py
+++ b/edalize/nextpnr.py
@@ -79,8 +79,8 @@ def configure_main(self):
         command += constraints + ['--json', depends] + output
 
         #CLI target
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         #GUI target
-        commands.add(command+['--gui'], ["build-gui"], [depends])
+        commands.add([command+['--gui']], [self.EdaCommands.Target("build-gui", phony=True)], [depends])
         self.commands = commands.commands
diff --git a/edalize/quartus.py b/edalize/quartus.py
index 3fe4c347c..17ce9febf 100644
--- a/edalize/quartus.py
+++ b/edalize/quartus.py
@@ -5,7 +5,6 @@
 import logging
 import os.path
 import os
-import platform
 import subprocess
 import re
 import xml.etree.ElementTree as ET
@@ -20,8 +19,6 @@ class Quartus(Edatool):
 
     # Define Standard edition to be our default version
     isPro = False
-    makefile_template = {False : "quartus-std-makefile.j2",
-                         True  : "quartus-pro-makefile.j2"}
 
     @classmethod
     def get_doc(cls, api_ver):
@@ -106,10 +103,8 @@ def __init__(self, edam=None, work_root=None, eda_api=None, verbose=False):
     def configure_main(self):
         (src_files, incdirs) = self._get_fileset_files(force_slash=True)
         self.jinja_env.filters['src_file_filter'] = self.src_file_filter
-        self.jinja_env.filters['qsys_file_filter'] = self.qsys_file_filter
 
         has_vhdl2008 = 'vhdlSource-2008' in [x.file_type for x in src_files]
-        has_qsys     = 'QSYS'            in [x.file_type for x in src_files]
 
         escaped_name = self.name.replace(".", "_")
 
@@ -125,51 +120,149 @@ def configure_main(self):
             'has_vhdl2008' : has_vhdl2008
         }
 
-        # Render Makefile based on detected version
-        self.render_template(self.makefile_template[self.isPro],
-                             'Makefile',
-                             { 'name'         : escaped_name,
-                               'src_files'    : src_files,
-                               'tool_options' : self.tool_options})
+        self._write_makefile(escaped_name, src_files)
 
         # Render the TCL project file
         self.render_template('quartus-project.tcl.j2',
                              escaped_name + '.tcl',
                              template_vars)
 
+    """ Write a the Makefile using EdaCommands from the base class
+    """
 
-    # Helper to extract file type
-    def file_type(self, f):
-        return f.file_type.split('-')[0]
+    def _write_makefile(self, escaped_name, src_files):
+        # Write Makefile
+        commands = self.EdaCommands()
+
+        # Add variables
+        #
+        # It would be better to make an official interface rather than muck with
+        # the header
+
+        commands.header += f"""NAME := {escaped_name}
+OPTIONS := {" ".join(self.tool_options["quartus_options"])}
+DSE_OPTIONS := {" ".join(self.tool_options["dse_options"])}
+
+"""
+
+        # Project file
+        depends = "$(NAME).tcl"
+        cmd = ["quartus_sh", "$(OPTIONS)", "-t", depends]
+        targets = [self.EdaCommands.Target("project", phony=True)]
+        commands.add([cmd], targets, [depends])
+
+        # Qsys
+        qsys_files = [f for f in src_files if f.file_type == "QSYS"]
+        depends = "project"
+        targets = [self.EdaCommands.Target("qsys", phony=True)]
+        cmds = []
+
+        for f in qsys_files:
+
+            # Give QSYS files special attributes to make the logic in
+            # the Jinja2 templates much simplier
+            setattr(f, "simplename", os.path.basename(f.name).split(".qsys")[0])
+            setattr(f, "srcdir", os.path.dirname(f.name) or ".")
+            setattr(f, "dstdir", os.path.join("qsys", f.simplename))
 
-    # Filter for just QSYS files. This verifies that they are compatible
-    # with the identified Quartus version
-    def qsys_file_filter(self, f):
-        name = ''
-        if self.file_type(f) == 'QSYS':
             # Compatibility checks
             try:
                 qsysTree = ET.parse(os.path.join(self.work_root, f.name))
                 try:
-                    tool = qsysTree.find('component').attrib['tool']
-                    if tool == 'QsysPro' and self.isPro:
-                        name = f.name
+                    tool = qsysTree.find("component").attrib["tool"]
+                    if not (tool == "QsysPro" and self.isPro):
+                        continue
                 except (AttributeError, KeyError):
                     # Either a component wasn't found in the QSYS file, or it
                     # had no associated tool information. Make the assumption
                     # it was a Standard edition file
-                    if not self.isPro:
-                        name = f.name
+                    if self.isPro:
+                        continue
             except (ET.ParseError, IOError):
                 logger.warning("Unable to parse QSYS file " + f.name)
 
-            # Give QSYS files special attributes to make the logic in
-            # the Jinja2 templates much simplier
-            setattr(f, "simplename", os.path.basename(f.name).split('.qsys')[0])
-            setattr(f, "srcdir", os.path.dirname(f.name) or '.')
-            setattr(f, "dstdir", os.path.join('qsys', f.simplename))
-        
-        return name
+            family = self.tool_options["family"]
+            device = self.tool_options["device"]
+            if self.isPro:
+                cmds.append(
+                    [
+                        "qsys-generate",
+                        f.name,
+                        "--synthesis=VERILOG",
+                        f'--family="{family}"',
+                        f"--part={device}",
+                        "--quartus-project=$(NAME)",
+                    ]
+                )
+            else:
+                cmds.append(
+                    [
+                        "ip-generate",
+                        f"--project-directory={f.srcdir}",
+                        f"--output-directory={f.dstdir}",
+                        f"--report-file=bsf:{f.dstdir}/{f.simplename}.bsf",
+                        f'--system-info=DEVICE_FAMILY="{family}"',
+                        f"--system-info=DEVICE={device}",
+                        f"--component-file={f.srcdir}/{f.simplename}.qsys",
+                    ]
+                )
+                cmds.append(
+                    [
+                        "ip-generate",
+                        f"--project-directory={f.srcdir}",
+                        f"--output-directory={f.dstdir}/synthesis",
+                        "--file-set=QUARTUS_SYNTH",
+                        f"--report-file=sopcinfo:{f.dstdir}/{f.simplename}.sopcinfo",
+                        f"--report-file=html:{f.dstdir}/{f.simplename}.html",
+                        f"--report-file=qip:{f.dstdir}/{f.simplename}.qip",
+                        f"--report-file=cmp:{f.dstdir}/{f.simplename}.cmp",
+                        "--report-file=svd",
+                        f'--system-info=DEVICE_FAMILY="{family}"',
+                        f"--system-info=DEVICE={device}",
+                        f"--component-file={f.srcdir}/{f.simplename}.qsys",
+                        "--language=VERILOG",
+                    ]
+                )
+
+        commands.add(cmds, targets, [depends])
+
+        # syn
+        if self.isPro:
+            syn = "quartus_syn"
+        else:
+            syn = "quartus_map"
+        cmd = [syn, "$(OPTIONS)", "$(NAME)"]
+        targets = [self.EdaCommands.Target("syn", phony=True)]
+        commands.add([cmd], targets, ["qsys"])
+
+        # fit, asm, sta
+        for target, depends in [("fit", "syn"), ("asm", "fit"), ("sta", "asm")]:
+            cmd = [f"quartus_{target}", "$(OPTIONS)", "$(NAME)"]
+            targets = [self.EdaCommands.Target(target, phony=True)]
+            commands.add([cmd], targets, [depends])
+
+        # DSE
+        cmd = ["quartus_dse", "$(NAME)", "$(DSE_OPTIONS)"]
+        targets = [self.EdaCommands.Target("dse", phony=True)]
+        commands.add([cmd], targets, ["syn"])
+
+        # clean
+        cmd = ["rm", "-rf", "*.*"]
+        if self.isPro:
+            cmd += ["qdb", "tmp-clearbox"]
+        else:
+            cmd += ["db", "incremental_db"]
+
+        targets = [self.EdaCommands.Target("clean", phony=True)]
+        commands.add([cmd], targets, [])
+
+        commands.set_default_target("sta")
+
+        commands.write(os.path.join(self.work_root, "Makefile"))
+
+    # Helper to extract file type
+    def file_type(self, f):
+        return f.file_type.split('-')[0]
 
     # Allow the templates to get source file information
     def src_file_filter(self, f):
@@ -181,7 +274,7 @@ def _append_library(f):
 
         def _handle_qsys(t, f):
             # Quartus Pro just passes QSYS files onto the compiler, but Standard
-            # expects to see them sepecified as QIP. The Makefile is responsible
+            # expects to see them specified as QIP. The Makefile is responsible
             # for creating that QIP file for Standard edition in a known place
             # which can be used below
             if self.isPro:
diff --git a/edalize/symbiflow.py b/edalize/symbiflow.py
index 5b255d02c..b8a118863 100644
--- a/edalize/symbiflow.py
+++ b/edalize/symbiflow.py
@@ -185,7 +185,7 @@ def configure_nextpnr(self):
             command += ['--device', device]
             command += ['--top', self.toplevel]
             command += [depends, targets]
-            commands.add(command, [targets], [depends])
+            commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
             depends = self.name+'.netlist'
             targets = self.name+'.phys'
@@ -196,14 +196,14 @@ def configure_nextpnr(self):
             command += ['--write', self.name+'.routed.json']
             command += ['--phys', targets]
             command += [nextpnr_options]
-            commands.add(command, [targets], [depends])
+            commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
             depends = self.name+'.phys'
             targets = self.name+'.fasm'
             command = ['python', '-m', 'fpga_interchange.fasm_generator']
             command += ['--schema_dir', '$(INTERCHANGE_SCHEMA_PATH)']
             command += ['--family', family, device, self.name+'.netlist', depends, targets]
-            commands.add(command, [targets], [depends])
+            commands.add([command], [self.EdaCommands.Target(targets)], [depends])
         else:
             targets = self.name+'.fasm'
             command = ['nextpnr-'+arch, '--chipdb', chipdb]
@@ -213,13 +213,13 @@ def configure_nextpnr(self):
             command += ['--fasm', targets]
             command += ['--log', 'nextpnr.log']
             command += [nextpnr_options]
-            commands.add(command, [targets], [depends])
+            commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         depends = self.name+'.fasm'
         targets = self.name+'.bit'
         command = ['symbiflow_write_bitstream', '-d', bitstream_device]
         command += ['-f', depends, '-p', partname, '-b', targets]
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         commands.set_default_target(targets)
         commands.write(os.path.join(self.work_root, 'Makefile'))
@@ -290,7 +290,7 @@ def configure_vpr(self):
         command += ['-d', bitstream_device]
         command += ['-p' if vendor == 'xilinx' else '-P', partname]
         command += xdc_opts
-        commands.add(command, [targets], [])
+        commands.add([command], [self.EdaCommands.Target(targets)], [])
 
         #P&R
         eblif_opt = ['-e', self.toplevel+'.eblif']
@@ -299,26 +299,26 @@ def configure_vpr(self):
         depends = self.toplevel+'.eblif'
         targets = self.toplevel+'.net'
         command = ['symbiflow_pack'] + eblif_opt + device_opt + sdc_opts + vpr_options
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         depends = self.toplevel+'.net'
         targets = self.toplevel+'.place'
         command = ['symbiflow_place'] + eblif_opt + device_opt
         command += ['-n', depends, '-P', partname]
         command += sdc_opts + pcf_opts + vpr_options
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         depends = self.toplevel+'.place'
         targets = self.toplevel+'.route'
         command = ['symbiflow_route'] + eblif_opt + device_opt
         command += sdc_opts + vpr_options
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         depends = self.toplevel+'.route'
         targets = self.toplevel+'.fasm'
         command = ['symbiflow_write_fasm'] + eblif_opt + device_opt
         command += sdc_opts + vpr_options
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         depends = self.toplevel+'.fasm'
         targets = self.toplevel+'.bit'
@@ -326,7 +326,7 @@ def configure_vpr(self):
         command += ['-f', depends]
         command += ['-p' if vendor == 'xilinx' else '-P', partname]
         command += ['-b', targets]
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         commands.set_default_target(targets)
         commands.write(os.path.join(self.work_root, 'Makefile'))
diff --git a/edalize/templates/quartus/quartus-pro-makefile.j2 b/edalize/templates/quartus/quartus-pro-makefile.j2
deleted file mode 100644
index ff06d0c31..000000000
--- a/edalize/templates/quartus/quartus-pro-makefile.j2
+++ /dev/null
@@ -1,34 +0,0 @@
-# Auto generated by Edalize
-NAME := {{ name }}
-OPTIONS := {{ tool_options.quartus_options|join(' ') }}
-DSE_OPTIONS := {{ tool_options.dse_options|join(' ') }}
-
-all: sta
-
-project: $(NAME).tcl
-	$(EDALIZE_LAUNCHER) quartus_sh $(OPTIONS) -t $(NAME).tcl
-
-qsys: project
-{% for qsys_file in src_files if qsys_file|qsys_file_filter %}
-	qsys-generate {{ qsys_file|qsys_file_filter }} --synthesis=VERILOG --family="{{ tool_options.family }}" --part={{ tool_options.device }} --quartus-project=$(NAME)
-{% endfor %}
-
-syn: qsys
-	$(EDALIZE_LAUNCHER) quartus_syn $(OPTIONS) $(NAME)
-
-fit: syn
-	$(EDALIZE_LAUNCHER) quartus_fit $(OPTIONS) $(NAME)
-
-asm: fit
-	$(EDALIZE_LAUNCHER) quartus_asm $(OPTIONS) $(NAME)
-
-sta: asm
-	$(EDALIZE_LAUNCHER) quartus_sta $(OPTIONS) $(NAME)
-
-dse: syn
-	$(EDALIZE_LAUNCHER) quartus_dse $(NAME) $(DSE_OPTIONS)
-
-clean:
-	$(EDALIZE_LAUNCHER) rm -rf *.* qdb tmp-clearbox
-
-.PHONY: all project qsys syn fit asm sta dse clean
diff --git a/edalize/templates/quartus/quartus-std-makefile.j2 b/edalize/templates/quartus/quartus-std-makefile.j2
deleted file mode 100644
index a7049d2ee..000000000
--- a/edalize/templates/quartus/quartus-std-makefile.j2
+++ /dev/null
@@ -1,35 +0,0 @@
-# Auto generated by Edalize
-NAME := {{ name }}
-OPTIONS := {{ tool_options.quartus_options|join(' ') }}
-DSE_OPTIONS := {{ tool_options.dse_options|join(' ') }}
-
-all: sta
-
-project: $(NAME).tcl
-	$(EDALIZE_LAUNCHER) quartus_sh $(OPTIONS) -t $(NAME).tcl
-
-qsys: project
-{% for qsys_file in src_files if qsys_file|qsys_file_filter %}
-	$(EDALIZE_LAUNCHER) ip-generate --project-directory={{qsys_file.srcdir}} --output-directory={{qsys_file.dstdir}} --report-file=bsf:{{qsys_file.dstdir}}/{{qsys_file.simplename}}.bsf --system-info=DEVICE_FAMILY="{{tool_options.family}}" --system-info=DEVICE={{tool_options.device}} --component-file={{qsys_file.srcdir}}/{{qsys_file.simplename}}.qsys
-	$(EDALIZE_LAUNCHER) ip-generate --project-directory={{qsys_file.srcdir}} --output-directory={{qsys_file.dstdir}}/synthesis --file-set=QUARTUS_SYNTH --report-file=sopcinfo:{{qsys_file.dstdir}}/{{qsys_file.simplename}}.sopcinfo --report-file=html:{{qsys_file.dstdir}}/{{qsys_file.simplename}}.html --report-file=qip:{{qsys_file.dstdir}}/{{qsys_file.simplename}}.qip --report-file=cmp:{{qsys_file.dstdir}}/{{qsys_file.simplename}}.cmp --report-file=svd --system-info=DEVICE_FAMILY="{{tool_options.family}}" --system-info=DEVICE={{tool_options.device}} --component-file={{qsys_file.srcdir}}/{{qsys_file.simplename}}.qsys --language=VERILOG
-{% endfor %}
-
-syn: qsys
-	$(EDALIZE_LAUNCHER) quartus_map $(OPTIONS) $(NAME)
-
-fit: syn
-	$(EDALIZE_LAUNCHER) quartus_fit $(OPTIONS) $(NAME)
-
-asm: fit
-	$(EDALIZE_LAUNCHER) quartus_asm $(OPTIONS) $(NAME)
-
-sta: asm
-	$(EDALIZE_LAUNCHER) quartus_sta $(OPTIONS) $(NAME)
-
-dse: syn
-	$(EDALIZE_LAUNCHER) quartus_dse $(NAME) $(DSE_OPTIONS)
-
-clean:
-	$(EDALIZE_LAUNCHER) rm -rf *.* db incremental_db
-
-.PHONY: all project qsys syn fit asm sta dse clean
diff --git a/edalize/trellis.py b/edalize/trellis.py
index 1102f693b..8d1eab09c 100644
--- a/edalize/trellis.py
+++ b/edalize/trellis.py
@@ -57,7 +57,7 @@ def configure_main(self):
         depends = self.name+'.config'
         targets = self.name+'.bit'
         command = ['ecppack', '--svf', self.name+'.svf', depends, targets]
-        commands.add(command, [targets], [depends])
+        commands.add([command], [self.EdaCommands.Target(targets)], [depends])
 
         commands.set_default_target(self.name+'.bit')
         commands.write(os.path.join(self.work_root, 'Makefile'))
diff --git a/edalize/vivado.py b/edalize/vivado.py
index b338f798c..a79907a10 100644
--- a/edalize/vivado.py
+++ b/edalize/vivado.py
@@ -183,25 +183,25 @@ def configure_main(self):
         #Create project file
         project_file = self.name+'.xpr'
         tcl_file = [self.name+'.tcl']
-        commands.add(vivado_command+tcl_file, [project_file], tcl_file + edif_files)
+        commands.add([vivado_command+tcl_file], [self.EdaCommands.Target(project_file)], tcl_file + edif_files)
 
         #Synthesis target
         if synth_tool == 'yosys':
             commands.commands += yosys.commands
-            commands.add([], ['synth'], edif_files)
+            commands.add([], [self.EdaCommands.Target('synth', phony=True)], edif_files)
         else:
             depends = [f'{self.name}_synth.tcl', project_file]
-            targets = [f'{self.name}.runs/synth_1/__synthesis_is_complete__']
-            commands.add(vivado_command+depends, targets, depends)
-            commands.add([], ['synth'], targets)
+            targets = [self.EdaCommands.Target(f'{self.name}.runs/synth_1/__synthesis_is_complete__')]
+            commands.add([vivado_command+depends], targets, depends)
+            commands.add([], [self.EdaCommands.Target('synth', phony=True)], targets)
 
         #Bitstream generation
         run_tcl = self.name+'_run.tcl'
         depends = [run_tcl, project_file]
         bitstream = self.name+'.bit'
-        commands.add(vivado_command+depends, [bitstream], depends)
+        commands.add([vivado_command+depends], [self.EdaCommands.Target(bitstream)], depends)
 
-        commands.add(['vivado', project_file], ['build-gui'], [project_file])
+        commands.add([['vivado', project_file]], [self.EdaCommands.Target('build-gui', phony=True)], [project_file])
 
         depends = [self.name+'_pgm.tcl', bitstream]
         command = ['vivado', '-quiet', '-nolog', '-notrace', '-mode', 'batch',
@@ -210,7 +210,7 @@ def configure_main(self):
         part = self.tool_options.get('part', "")
         command += [part] if part else []
         command += [bitstream]
-        commands.add(command, ['pgm'], depends)
+        commands.add([command], [self.EdaCommands.Target('pgm', phony=True)], depends)
 
         commands.set_default_target(bitstream)
         commands.write(os.path.join(self.work_root, 'Makefile'))
diff --git a/edalize/yosys.py b/edalize/yosys.py
index ec7ca7221..f427e8459 100644
--- a/edalize/yosys.py
+++ b/edalize/yosys.py
@@ -117,8 +117,8 @@ def configure_main(self):
                                  template_vars)
 
         commands = self.EdaCommands()
-        commands.add(['yosys', '-l', 'yosys.log', '-p', f'"tcl {template}"'],
-                         [f'{self.name}.{output}' for output in ['blif', 'json','edif']],
+        commands.add([['yosys', '-l', 'yosys.log', '-p', f'"tcl {template}"']],
+                         [self.EdaCommands.Target(f'{self.name}.{output}') for output in ['blif', 'json','edif']],
                          [template])
         if self.tool_options.get('yosys_as_subtool'):
             self.commands = commands.commands
diff --git a/setup.py b/setup.py
index 056af49c8..7519ab990 100644
--- a/setup.py
+++ b/setup.py
@@ -25,8 +25,6 @@ def read(fname):
         'templates/vivado/vivado-synth.tcl.j2',
         'templates/vunit/run.py.j2',
         'templates/quartus/quartus-project.tcl.j2',
-        'templates/quartus/quartus-std-makefile.j2',
-        'templates/quartus/quartus-pro-makefile.j2',
         'templates/ascentlint/Makefile.j2',
         'templates/ascentlint/run-ascentlint.tcl.j2',
         'templates/libero/libero-project.tcl.j2',
diff --git a/tests/test_apicula/Makefile b/tests/test_apicula/Makefile
index 83548a080..c3b09e608 100644
--- a/tests/test_apicula/Makefile
+++ b/tests/test_apicula/Makefile
@@ -13,3 +13,5 @@ build-gui: test_apicula_0.json
 
 test_apicula_0.fs: test_apicula_0.pack
 	$(EDALIZE_LAUNCHER) gowin_pack -d GW1N-LV1QN48C6/I5 -o test_apicula_0.fs test_apicula_0.pack
+
+.PHONY: all build-gui
diff --git a/tests/test_apicula/minimal/Makefile b/tests/test_apicula/minimal/Makefile
index e524981a5..ee8156d55 100644
--- a/tests/test_apicula/minimal/Makefile
+++ b/tests/test_apicula/minimal/Makefile
@@ -13,3 +13,5 @@ build-gui: test_apicula_0.json
 
 test_apicula_0.fs: test_apicula_0.pack
 	$(EDALIZE_LAUNCHER) gowin_pack -d GW1N-LV1QN48C6/I5 -o test_apicula_0.fs test_apicula_0.pack
+
+.PHONY: all build-gui
diff --git a/tests/test_icestorm/Makefile b/tests/test_icestorm/Makefile
index 81324df45..a0abc60e4 100644
--- a/tests/test_icestorm/Makefile
+++ b/tests/test_icestorm/Makefile
@@ -23,3 +23,5 @@ test_icestorm_0.stat: test_icestorm_0.asc
 	$(EDALIZE_LAUNCHER) icebox_stat test_icestorm_0.asc test_icestorm_0.stat
 
 stats: test_icestorm_0.stat
+
+.PHONY: all build-gui timing stats
diff --git a/tests/test_icestorm/minimal/Makefile b/tests/test_icestorm/minimal/Makefile
index 81324df45..a0abc60e4 100644
--- a/tests/test_icestorm/minimal/Makefile
+++ b/tests/test_icestorm/minimal/Makefile
@@ -23,3 +23,5 @@ test_icestorm_0.stat: test_icestorm_0.asc
 	$(EDALIZE_LAUNCHER) icebox_stat test_icestorm_0.asc test_icestorm_0.stat
 
 stats: test_icestorm_0.stat
+
+.PHONY: all build-gui timing stats
diff --git a/tests/test_icestorm/nextpnr/Makefile b/tests/test_icestorm/nextpnr/Makefile
index 9585e299d..38af285be 100644
--- a/tests/test_icestorm/nextpnr/Makefile
+++ b/tests/test_icestorm/nextpnr/Makefile
@@ -23,3 +23,5 @@ test_icestorm_0.stat: test_icestorm_0.asc
 	$(EDALIZE_LAUNCHER) icebox_stat test_icestorm_0.asc test_icestorm_0.stat
 
 stats: test_icestorm_0.stat
+
+.PHONY: all build-gui timing stats
diff --git a/tests/test_quartus/Pro/Makefile b/tests/test_quartus/Pro/Makefile
index 516d6d67f..3a65943d8 100644
--- a/tests/test_quartus/Pro/Makefile
+++ b/tests/test_quartus/Pro/Makefile
@@ -1,4 +1,5 @@
-# Auto generated by Edalize
+#Auto generated by Edalize
+
 NAME := test_quartus_0
 OPTIONS := some quartus_options
 DSE_OPTIONS := some dse_options
@@ -9,7 +10,7 @@ project: $(NAME).tcl
 	$(EDALIZE_LAUNCHER) quartus_sh $(OPTIONS) -t $(NAME).tcl
 
 qsys: project
-	qsys-generate qsys_file --synthesis=VERILOG --family="Cyclone V" --part=5CSXFC6D6F31C8ES --quartus-project=$(NAME)
+	$(EDALIZE_LAUNCHER) qsys-generate qsys_file --synthesis=VERILOG --family="Cyclone V" --part=5CSXFC6D6F31C8ES --quartus-project=$(NAME)
 
 syn: qsys
 	$(EDALIZE_LAUNCHER) quartus_syn $(OPTIONS) $(NAME)
diff --git a/tests/test_quartus/Standard/Makefile b/tests/test_quartus/Standard/Makefile
index 2e2f91467..4be2671d9 100644
--- a/tests/test_quartus/Standard/Makefile
+++ b/tests/test_quartus/Standard/Makefile
@@ -1,4 +1,5 @@
-# Auto generated by Edalize
+#Auto generated by Edalize
+
 NAME := test_quartus_0
 OPTIONS := some quartus_options
 DSE_OPTIONS := some dse_options
diff --git a/tests/test_reporting.py b/tests/test_reporting.py
index 05f515a32..21a1d3b02 100644
--- a/tests/test_reporting.py
+++ b/tests/test_reporting.py
@@ -293,7 +293,7 @@ def test_picorv32_ise_spartan6_resources(picorv32_s6_data):
     # Check Control Set Information table
     df = rpt["Control Set Information"]
 
-    assert df["Clock Signal"].all() == "clk_BUFGP"
+    assert (df["Clock Signal"] == "clk_BUFGP").all()
     assert df.shape == (20, 6)
 
     rst_en = df[
@@ -672,7 +672,7 @@ def test_linux_on_litex_vexriscv_pipistrello_resources(
     df = rpt["IOB Properties"].set_index("IOB Name")
 
     ddr_io = df.filter(regex="ddram_*", axis=0)
-    assert ddr_io["IO Standard"].all() == "MOBILE_DDR"
+    assert (ddr_io["IO Standard"] == "MOBILE_DDR").all()
 
     # Check Control Set Information table
     df = rpt["Control Set Information"]
diff --git a/tests/test_symbiflow/nextpnr/fpga_interchange/Makefile b/tests/test_symbiflow/nextpnr/fpga_interchange/Makefile
index 45f8c956d..f759d16e1 100644
--- a/tests/test_symbiflow/nextpnr/fpga_interchange/Makefile
+++ b/tests/test_symbiflow/nextpnr/fpga_interchange/Makefile
@@ -20,3 +20,5 @@ test_symbiflow_nextpnr_fpga_interchange_0.fasm: test_symbiflow_nextpnr_fpga_inte
 
 test_symbiflow_nextpnr_fpga_interchange_0.bit: test_symbiflow_nextpnr_fpga_interchange_0.fasm
 	$(EDALIZE_LAUNCHER) symbiflow_write_bitstream -d artix7 -f test_symbiflow_nextpnr_fpga_interchange_0.fasm -p xc7a35tcsg324-1csg324-1 -b test_symbiflow_nextpnr_fpga_interchange_0.bit
+
+.PHONY: all
diff --git a/tests/test_symbiflow/nextpnr/xilinx/Makefile b/tests/test_symbiflow/nextpnr/xilinx/Makefile
index edb6d337d..0684f42e6 100644
--- a/tests/test_symbiflow/nextpnr/xilinx/Makefile
+++ b/tests/test_symbiflow/nextpnr/xilinx/Makefile
@@ -10,3 +10,5 @@ test_symbiflow_nextpnr_xilinx_0.fasm: test_symbiflow_nextpnr_xilinx_0.json
 
 test_symbiflow_nextpnr_xilinx_0.bit: test_symbiflow_nextpnr_xilinx_0.fasm
 	$(EDALIZE_LAUNCHER) symbiflow_write_bitstream -d artix7 -f test_symbiflow_nextpnr_xilinx_0.fasm -p xc7a35tcsg324-1csg324-1 -b test_symbiflow_nextpnr_xilinx_0.bit
+
+.PHONY: all
diff --git a/tests/test_symbiflow/vtr/Makefile b/tests/test_symbiflow/vtr/Makefile
index fe3f6604a..6218b6cbe 100644
--- a/tests/test_symbiflow/vtr/Makefile
+++ b/tests/test_symbiflow/vtr/Makefile
@@ -19,3 +19,5 @@ top_module.fasm: top_module.route
 
 top_module.bit: top_module.fasm
 	$(EDALIZE_LAUNCHER) symbiflow_write_bitstream -d artix7 -f top_module.fasm -p xc7a35tcsg324-1csg324-1 -b top_module.bit
+
+.PHONY: all
diff --git a/tests/test_trellis/Makefile b/tests/test_trellis/Makefile
index e645b2dce..be74133fb 100644
--- a/tests/test_trellis/Makefile
+++ b/tests/test_trellis/Makefile
@@ -13,3 +13,5 @@ build-gui: test_trellis_0.json
 
 test_trellis_0.bit: test_trellis_0.config
 	$(EDALIZE_LAUNCHER) ecppack --svf test_trellis_0.svf test_trellis_0.config test_trellis_0.bit
+
+.PHONY: all build-gui
diff --git a/tests/test_trellis/minimal/Makefile b/tests/test_trellis/minimal/Makefile
index 8ca6acecf..47fe33776 100644
--- a/tests/test_trellis/minimal/Makefile
+++ b/tests/test_trellis/minimal/Makefile
@@ -13,3 +13,5 @@ build-gui: test_trellis_0.json
 
 test_trellis_0.bit: test_trellis_0.config
 	$(EDALIZE_LAUNCHER) ecppack --svf test_trellis_0.svf test_trellis_0.config test_trellis_0.bit
+
+.PHONY: all build-gui
diff --git a/tests/test_vivado/Makefile b/tests/test_vivado/Makefile
index 614dc7c66..8f18afcd4 100644
--- a/tests/test_vivado/Makefile
+++ b/tests/test_vivado/Makefile
@@ -18,3 +18,5 @@ build-gui: test_vivado_0.xpr
 
 pgm: test_vivado_0_pgm.tcl test_vivado_0.bit
 	$(EDALIZE_LAUNCHER) vivado -quiet -nolog -notrace -mode batch -source test_vivado_0_pgm.tcl -tclargs xc7a35tcsg324-1 test_vivado_0.bit
+
+.PHONY: all synth build-gui pgm
diff --git a/tests/test_vivado/minimal/Makefile b/tests/test_vivado/minimal/Makefile
index 73d38c2b6..2a22f5308 100644
--- a/tests/test_vivado/minimal/Makefile
+++ b/tests/test_vivado/minimal/Makefile
@@ -18,3 +18,5 @@ build-gui: test_vivado_minimal_0.xpr
 
 pgm: test_vivado_minimal_0_pgm.tcl test_vivado_minimal_0.bit
 	$(EDALIZE_LAUNCHER) vivado -quiet -nolog -notrace -mode batch -source test_vivado_minimal_0_pgm.tcl -tclargs xc7a35tcsg324-1 test_vivado_minimal_0.bit
+
+.PHONY: all synth build-gui pgm
diff --git a/tests/test_vivado/yosys/Makefile b/tests/test_vivado/yosys/Makefile
index 0c75202ee..251754150 100644
--- a/tests/test_vivado/yosys/Makefile
+++ b/tests/test_vivado/yosys/Makefile
@@ -18,3 +18,5 @@ build-gui: test_vivado_yosys_0.xpr
 
 pgm: test_vivado_yosys_0_pgm.tcl test_vivado_yosys_0.bit
 	$(EDALIZE_LAUNCHER) vivado -quiet -nolog -notrace -mode batch -source test_vivado_yosys_0_pgm.tcl -tclargs xc7a35tcsg324-1 test_vivado_yosys_0.bit
+
+.PHONY: all synth build-gui pgm