These are chat archives for nextflow-io/nextflow

22nd
Jan 2019
Paolo Di Tommaso
@pditommaso
Jan 22 07:36
no
@tdudgeon Yes, correct. When using grid engine or similar executor NF does not take care to stage (remotely) the task scripts
Yasset Perez-Riverol
@ypriverol
Jan 22 13:13

Im receiving this error:

WARN: Input tuple does not match input set cardinality declared by process

Does anyone has idea? Here the script.

/**
 * Compile all the results in to one xml file.
 */
 process mergeCompleteSearchResults {
     container 'ypriverol/pia:1.3.10'
     publishDir "result"

     memory { 16.GB * task.attempt }
     errorStrategy 'retry'

     input:
     set file(input_files) from all_search_files.collect()

     output:
     file "*.xml" into merged_pia_compilation

     script:
     """
     pia -Xmx${10 * task.attempt}g compiler -infile ${(input_files as List).join(" -infile ")} -name pia-fina-complete -outfile pia-final-merged.xml
     """
 }
Paolo Di Tommaso
@pditommaso
Jan 22 13:15
replace set file(input_files) with file(input_files)
set is only used when n-tuple, n>1
Yasset Perez-Riverol
@ypriverol
Jan 22 13:16
I have changed and I have a new error input file name collision -- There are multiple input files for each of the following file names: test.mgf.xml, test.mzid, crap-test.mzid, crap-test.mgf.xml
Paolo Di Tommaso
@pditommaso
Jan 22 13:17
it means what it says, there's a file name collision on your input set
Yasset Perez-Riverol
@ypriverol
Jan 22 13:17
ok
Paolo Di Tommaso
@pditommaso
Jan 22 13:17
crap-test.mgf.xml :satisfied:
Yasset Perez-Riverol
@ypriverol
Jan 22 13:17
jajajajajaj ;)
checking now thanks @pditommaso
Paolo Di Tommaso
@pditommaso
Jan 22 13:18
welcome
Yasset Perez-Riverol
@ypriverol
Jan 22 13:42
Problem solve thanks @pditommaso
Paolo Di Tommaso
@pditommaso
Jan 22 14:15
:v:
micans
@micans
Jan 22 15:35
Nice work again! :fireworks:
Paolo Di Tommaso
@pditommaso
Jan 22 15:36
:v: