yanlinlin82 / seqpipe

A framework for SEQuencing data analysis PIPElines.
http://yanlinlin82.github.io/seqpipe/
MIT License
7 stars 4 forks source link

Dependency checking error when step has only output without input #13

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago
**What steps will reproduce the problem?**

1. Use pipeline script as following:

$ cat foo.pipe function foo {

[input="${A}" output="${B}"]

cat ${A} > ${B}
#[output="${C}"]
date > ${C}
#[input="${B}" input="${C}" output="${D}"]
cat ${B} ${C} > ${D}

}


2. Run command:

$ seqpipe -m foo.pipe foo -h A=a B=b C=c D=d

Input file(s): a Definition: ${A} c Definition: ${C}

Output file(s): d Definition: ${D}

NOTE: Use '-H' option to see all variables for procedure 'foo'.


3. Here, "${C}" is wrongly treated as input rather than output or intermediate 
file.

**What is the expected output? What do you see instead?**

It is expected that "${C}" is not input of the whole pipeline.

Original issue reported on code.google.com by yanlinlin82 on 18 Jun 2013 at 2:28

GoogleCodeExporter commented 9 years ago
Fixed in r342.

Original comment by yanlinlin82 on 28 Sep 2013 at 3:15