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rule all:
input: "simple_shallow.out", "simple_full.out",
"absolute_exists.out", "touched.out", "log_exists.out",
"protected.out", "benchmark_exists.out", "minimal_ok.out"
rule shallow:
input: "test.in"
output: "simple_shallow.out"
shadow: "shallow"
shell:
"""
echo 1 > junk.out
cat {input} >> {output}
echo simple_shallow >> {output}
test ! -f more_junk.out
"""
rule full:
input: "test.in"
output: "simple_full.out"
shadow: "full"
shell:
"""
echo 1 > more_junk.out
cat {input} > {output}
echo simple_full >> {output}
test ! -f junk.out
"""
rule absolute_link:
input: "test.in"
output: "absolute.out", "absolute_link.out"
shadow: "shallow"
shell:
"""
echo 1 > absolute.out
DIRNAME=$(perl -e 'use Cwd "abs_path"; print abs_path(shift)' .)
ln -s $DIRNAME/absolute.out absolute_link.out
"""
# Snakemake has check_broken_symlink so we just need to test existence
rule absolute_stat:
input: "absolute_link.out"
output: touch("absolute_exists.out")
shell:
"""
test -f {input}
"""
rule log_stat:
input: "touched.out"
output: touch("log_exists.out")
shell:
"""
test -f shadow.log
"""
rule touch:
output: touch("touched.out")
log: "shadow.log"
shadow: "shallow"
shell:
"""
echo 1 > {log}
"""
rule protected:
output: protected("protected.out")
shadow: "shallow"
shell:
"""
touch {output}
"""
rule benchmark:
output: touch("benchmark.out")
benchmark: "benchmark.txt"
shadow: "shallow"
shell:
"""
touch {output}
"""
rule benchmark_stat:
input: "benchmark.out"
output: touch("benchmark_exists.out")
shell:
"""
test -f benchmark.txt
"""
# Setup files for testing of shadow: "minimal"
rule minimal_setup:
input: "test.in"
output:
"subdir1/subdir2/test.in",
"subdir1/subdir2/test.symbolic.in"
shell:
"""
cp -P {input} {output[0]}
cd subdir1/subdir2
ln -s test.in test.symbolic.in
"""
# Tests relative inputs/outputs and in the current dir
rule minimal_rel_curdir:
input: "test.in"
output: protected("simple_minimal.out")
benchmark: "benchmark_minimal.txt"
log: "minimal.log"
shadow: "minimal"
shell:
"""
touch minimal_junk.out
cat {input} >> {output}
echo simple_minimal >> {output}
echo minimal_log > {log}
"""
# Tests relative inputs/outputs in subdirectories
rule minimal_rel_subdir:
input: "subdir1/subdir2/test.in"
output: "outdir/minimal.out"
shadow: "minimal"
shell:
"""
touch outdir/minimal_junk.out
touch {output}
"""
# Tests symbolic input/output
rule minimal_symbolic:
input: "subdir1/subdir2/test.symbolic.in"
output: "outdir/minimal_real.out",
"outdir/minimal_symbolic.out"
shadow: "minimal"
shell:
"""
touch outdir/minimal_real.out
cd outdir
ln -s minimal_real.out minimal_symbolic.out
"""
# Tests absolute input/output
rule minimal_absolute:
input:
os.path.join(os.getcwd(),"test.in")
output: os.path.join(os.getcwd(),"outdir/minimal_absolute.out")
shadow: "minimal"
shell:
"""
touch {output}
"""
# Aggregates tests for shadow: "minimal"
rule minimal_ok:
input: "simple_minimal.out",
"outdir/minimal.out",
"outdir/minimal_symbolic.out",
os.path.join(os.getcwd(),"outdir/minimal_absolute.out")
output: "minimal_ok.out"
shell:
"""
#test ! -w {input[0]}
test -f benchmark_minimal.txt
test -f minimal.log
test ! -f minimal_junk.out
test ! -f outdir/minimal_junk.out
touch {output}
"""
|
