jstaut
commented
9 months ago We suspect that one of the input files is either missing or incorrectly typed in the config file (mismatch between the actual file name and the name in the config). Probably the problem is in the name of your cells2cluster file (please check carefully if the name and path of that file is corresponding to the one in the config file). Alternatively, it could also be that the path to the expression matrix is wrong. So please check whether the path to both files is completely correct. FYI: we already have implemented a fix so that incorrect file names will, in the future, throw an error instead of simply finishing the pipeline as you showed. This will be released soon in MINI-EX version 2.2.
If this does not solve the problem, could you please show us the content of your input folder (ls -l /work/user/kwang/MINI-EX/tomato/INPUTS/) so we can have a closer look, and we will get back to you.
Hello,
I ran the following script to analyze the MINI-EX job. The job completed without any issues, but certain processes were not executed. I would greatly appreciate it if you could help me identify how I can correct my script. Thank you.
my script:
or
nextflow -C miniex_run_slurm.config run miniex.nfminiex_run_slurm.config:
` executor { name = 'slurm' queueSize = 5 }
process.container = "vibpsb/mini-ex:latest" singularity { enabled = true cacheDir = "singularity_cache" autoMounts = true }
params { expressionMatrix = "$baseDir/tomato/INPUTS/_matrix.txt" markersOut = "$baseDir/tomato/INPUTS/_allMarkers.txt" cell2clusters = "$baseDir/tomato/INPUTS/_cells2clusters.txt" cluster2ident = "$baseDir/tomato/INPUTS/_identities.txt" TF_list = "$baseDir/tomato/INPUTS/TF_list.txt" //termsOfInterest = "$baseDir/tomato/INPUTS/GOsIwant.txt" termsOfInterest = null
script_makeborda = "$baseDir/bin/MINIEX_makeBorda.py" script_scoreEdges = "$baseDir/bin/MINIEX_scoreEdges.py" script_heatmapTops = "$baseDir/bin/MINIEX_visual_heatmap_top150.py" script_regmaps = "$baseDir/bin/MINIEX_regmap.py"
}
process {
} `
nf report: