SNP annotation : false #2
Description
Hello,
Thank you for all your work!
I am trying to use this PredictDB-nextflow but I always had this error even with the example dataset:
Missing fromPath parameter -- Check script 'main.nf' at line: 94 or see '.nextflow.log' file for more details
and the SNP annotation : false
I use this commands:
$ module load cesga/system miniconda3/22.11.1-1
$ conda activate env_name
$ NXF_OPTS='-Xms1g -Xmx4g'
$nextflow run main.nf --gene_annotation /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/gene_annot.parsed.txt --snp_annot /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/snp_annot.chr*.txt --genotype /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/genotype.chr*.txt --gene_exp /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/gene_exp.csv --covariates /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/covariates.txt
and this is the result:
N E X T F L O W ~ version 23.10.1 Launching main.nf [irreverent_ride] DSL2 - revision: b024122f78 Run Name : irreverent_ride Gene annotation : /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/gene_annot.parsed.txt SNP annotation : false Expression file : /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/gene_exp.csv Genotype file : /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/genotype.chr10.txt Covariates : /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/MetaXcan_tutorial/data_predictdb/output/covariates.txt Max Resources : 480 GB memory, 48 cpus, 10d time per job Output dir : ./results Launch dir : /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/PredictDb-nextflow Working dir : /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/PredictDb-nextflow/work Script dir : /mnt/lustre/scratch/nlsas/home/otras/fmx/fgs/PredictDb-nextflow