Parameter validation failed for --hic

[GallVp]

Description of the bug

ERROR ~ Validation of pipeline parameters failed!

-- Check '.nextflow.log' file for details
The following invalid input values have been detected:

• --hic (SB1031HiC1.fastq.gz): "SB1031HiC1.fastq.gz" does not match regular expression [^SR\w+$|^\S+\{1,2\}[\w\.]*\.f(ast)?q\.gz$]

Command used and terminal output

nextflow run plant-food-research-open/assemblyqc \
-revision 2.2.0  \
-profile singularity \
--hic SB1031HiC{1,2}.fastq.gz

Relevant files

No response

System information

plant-food-research-open/assemblyqc -revision 2.2.0

[GallVp]

This issue arises from the bash expansion operator {}. Bash can be stopped from expanding the HiC files by wrapping it in double quotes as,

—hic "SB1031HiC{1,2}.fastq.gz”

Otherwise, the pipeline sees the following input,

—hic SB1031HiC1.fastq.gz SB1031HiC2.fastq.gz

and the trouble with Nextflow is that it does not pick up multiple arguments for one parameter.

[annabel-NZ]

Although this solution fixes the initial input validation step, I am still failing to get the pipeline to treat the HiC input as I would like. The fastq files are in the local directory (but as sym links) The pipeline is failing and seems to be attempting to source these inputs from SRA.

ERROR ~ Error executing process > 'PLANTFOODRESEARCHOPEN_ASSEMBLYQC:ASSEMBLYQC:FETCHNGS:SRATOOLS_PREFETCH (SB1031HiC{1,2}.fastq.gz)'

Caused by:
  Process `PLANTFOODRESEARCHOPEN_ASSEMBLYQC:ASSEMBLYQC:FETCHNGS:SRATOOLS_PREFETCH (SB1031HiC{1,2}.fastq.gz)` terminated with an error exit status (1)

[GallVp]

Thank you @annabel-NZ

This is a bug in the pipeline logic unfortunately due to the following logic,

assemblyqc/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf

Line 89 in 0141925

"$params.hic".find(/.*[\/].*\.(fastq|fq)\.gz/)

It expects that the fastq files will be nested under some path. To get around this, please try,

--hic "./SB1031HiC{1,2}.fastq.gz”

as the files are in the current directory (./). I'll try to fix it in the next update.