Hi !
I'm looking for a way to improve my pipeline ...
# nf-testl
Louis Le Nézet
12/10/2025, 2:17 PMHi !
I'm looking for a way to improve my pipeline level nf-test.
To do so I would like to share a common function to recursively check all the file in the output directory.
To share it I wa thinking of adding it to a groovy file in the libDir folder defined in the .nf-test.config but I didn't succeed in properly importing it.
Is there an example somewhere I could take inspiration from ?
Louis Le Nézet
12/10/2025, 2:18 PMHere is the function set in ./tests/lib/test_helper.groovy
Copy code
public class Methods {
public static def getRecursiveFileNames(fileOrDir, outputDir, variants_md5=true, txt_md5=true) {
def f = new File(fileOrDir.toString())
if ( f.isDirectory() ) {
return f.listFiles()
.collect { getRecursiveFileNames(it, outputDir, variants_md5) }
.sort { it.file }
}
def check = null
def file_name = f.toString().replace("${outputDir}/","")
if ( (f.name.endsWith('.txt') || f.name.endsWith('.log')) && txt_md5 ) {
check = path(f.toString()).md5
return ["file": file_name, "md5": check ]
} else if ( f.name.endsWith('.vcf.gz') && variants_md5 ) {
check = path(f.toString()).vcf.variantsMD5
return ["file": file_name, "variants": check ]
} else{
return ["file": file_name]
}
}
}Louis Le Nézet
12/10/2025, 2:20 PMI'm getting the following error when using it in a nextflow_pipeline test:
groovy.lang.MissingMethodException: No signature of method: test_stitch_nf$_run_closure1$_closure2.getRecursiveFileNames() is applicable for argument types: (sun.nio.fs.UnixPath, String) values: [/homem
Maxime Garcia
12/10/2025, 2:25 PMWhy not using https://nf-co.re/nft-utils#getallfilesfromdir ?
l
Louis Le Nézet
12/10/2025, 2:26 PMBecause I would like to obtain the md5sum of the variants when it's a vcf 🙂
m
Maxime Garcia
12/10/2025, 2:26 PMso my answer as often is Sarek
👀 1
Maxime Garcia
12/10/2025, 2:27 PMbut I have a simpler example in rnavar
Maxime Garcia
12/10/2025, 2:27 PMMaxime Garcia
12/10/2025, 2:28 PMl
Louis Le Nézet
12/10/2025, 2:31 PMThanks a lot.
The issue was that my groovy file wasn't named the same way as the class 🤣
m
Maxime Garcia
12/10/2025, 4:48 PMNice