I am useing nf-core/slamseq pipeline. I have encountered a constant error when I specify the “--skip_trimming true ” parameter. If I do not skip and use the --trim5 option, then there is no problem. the error message.
No such variable: Exception evaluating property 'reads' for nextflow.util.ArrayTuple, Reason: groovy.lang.MissingPropertyException: No such property: reads for class: sun.nio.fs.UnixPath
Possible solutions: class
-- Check script '/crex/proj/sllstore2017018/private/project/Trans_mem/nextflow/assets/nf-core/slamseq/main.nf' at line: 351 or see '.nextflow.log' file for more details
-[nf-core/slamseq] Pipeline completed with errors-
WARN: Killing pending tasks (1)
And corresponding code in line 351 as following
346 /*
347 * STEP 1 - TrimGalore!
348 /
349 if (params.skip_trimming) {
350 rawFiles
351 .map{ it -> return tuple(it, file(it.reads)) }
352 .set{ trimmedFiles }
353 trimgaloreQC = Channel.empty()