nf-core
getting issue when running default design csv with --genome GRCh37
Hi, I struggle to understand whats happening. I am running the pipeline from cloned github repo since I may need to adjust and implement a few aditional steps. The design.csv is the same in both occassion and is a default file for testing the pipeline.
When I run nextflow run ./nf-core/atacseq -profile cambridge,test --input ./design.csv all works ok,
But when I try to run with a full genome by nextflow run ./nf-core/atacseq -profile cambridge --input ./design.csv --genome GRCh37 I get an error on MERGED_LIB_CONSENSUS-
`*****
***** ERROR: Requested column 2, but database file - only has fields 1 - 0.
Warning message:
package ‘optparse’ was built under R version 3.6.3
Warning message:
package ‘UpSetR’ was built under R version 3.6.3
Error in read.table(opt$input_file, sep = "\t", header = FALSE) :
no lines available in input
Execution halted`
Is the sample data not compatible with the GRCh37? I tried also --genome hg19 but same issue appears. I can see that in the failed runs the consensus_peaks.mLb.clN.saf / OSMOTIC_STRESS_T15_R2* and all others are empty, indicating that the peaks have not been called correctly with the GRCh37. Hope you can help me. Thanks
