Hi! First of all thanks for developing and maintaining the nf-core/hic pipeline!
I have got a very strange issue that has driven me crazy for a while. Maybe there is something very obvious I am not seeing, so if that is the case, please disregard all of this 😅
After a lot of trial and error I have isolated how to reproduce it, but I am still a bit puzzled as to why exactly it happens. It seems to have something to do with similar group names, which I see is not necessarily ideal, but there are many circumstances I can think of where this would happen, so that is why I thought it would be useful to report. If there is a reason why not to allow names like this in the downstream process, then I would hope for a more informative error message.
So my minimal reproducible design table example (design_error.csv in the attached zip) looks like this:
Note that I only added a leading zero in the first line, so sample name group_1_mES now is group_01_mES.
Success! It is running:
executor > local (3)
[55/5cb224] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (design.csv) [100%] 1 of 1 ✔
I have reproduced this locally with docker on my computer, but I got the same exact error on uppmax with -profile uppmax option
Command used and terminal output
nextflow run nf-core/hic -profile docker --outdir ./mydata -r 2.0.0 --input design_error.csv --digestion mboi --genome mm10
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (design.csv)'
Caused by:
Process `NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (design.csv)` terminated with an error exit status (1)
Command executed:
check_samplesheet.py \
design.csv \
samplesheet.valid.csv
cat <<-END_VERSIONS > versions.yml
"NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK":
python: $(python --version | sed 's/Python //g')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
[CRITICAL] The given sample sheet does not appear to contain a header.
Work dir:
/home/carmen/work/experiments/230509_reproduce_error/work/b7/09d1541d09cf52115ea54ccb0ff0f2
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Description of the bug
Hi! First of all thanks for developing and maintaining the nf-core/hic pipeline!
I have got a very strange issue that has driven me crazy for a while. Maybe there is something very obvious I am not seeing, so if that is the case, please disregard all of this 😅
After a lot of trial and error I have isolated how to reproduce it, but I am still a bit puzzled as to why exactly it happens. It seems to have something to do with similar group names, which I see is not necessarily ideal, but there are many circumstances I can think of where this would happen, so that is why I thought it would be useful to report. If there is a reason why not to allow names like this in the downstream process, then I would hope for a more informative error message.
So my minimal reproducible design table example (
design_error.csv
in the attached zip) looks like this:And in my
./fastq
directory I have in fact those files:I run the pipeline and I get an error in the
NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK
process that reads:Now the interesting part is that if I change ever so slightly the naming of the groups (
design_success.csv
in the attached zip):Note that I only added a leading zero in the first line, so sample name
group_1_mES
now isgroup_01_mES
.Success! It is running:
I have reproduced this locally with docker on my computer, but I got the same exact error on uppmax with
-profile uppmax
optionCommand used and terminal output
Relevant files
mre_data.zip nextflow.log
System information
Nextflow version 23.04.1 Desktop Dell Precision 5820 Tower
Executor: local Container engine: Docker OS: Ubuntu 22.04.2 LTS (but also HPC - Uppmax + Singularity) nf-core/hic version 2.0.0