In some of the pipelines we already have some verbosity options included, see BIMSBbioinfo/pigx_bsseq#107.
Here we added the snakemake commands --printshellcmds and --verbose directly as arguments.
As Rekado actually pointed out there are different levels of verbosity, a nice example is shown here how it could be done and what the levels mean.
Maybe at some point we could decide on the different levels,
but I would like to already propose a structure, with lower numbers meaning lower verbosity:
- quiet: do not print anything to the screen, (maybe redirect all output into a log file )
- using the fmt() function from bsseq to print a helpful message
- normal snakemake output, if no message is set:
e.g.
input: /home/agosdsc/pigx/pigx_chipseq/Tests/in/ChIP.fq.gz
output: /home/agosdsc/pigx/pigx_chipseq/Tests/out_cluster/Trimmed/Trim_Galore/ChIP1/ChIP1_R.fastq.gz
log: /home/agosdsc/pigx/pigx_chipseq/Tests/out_cluster/Log/trim_galore_ChIP1.log
jobid: 3
wildcards: sample=ChIP1
--printshellcmds--verbose
In some of the pipelines we already have some verbosity options included, see BIMSBbioinfo/pigx_bsseq#107.
Here we added the snakemake commands
--printshellcmdsand--verbosedirectly as arguments.As Rekado actually pointed out there are different levels of verbosity, a nice example is shown here how it could be done and what the levels mean.
Maybe at some point we could decide on the different levels,
but I would like to already propose a structure, with lower numbers meaning lower verbosity:
e.g.
--printshellcmds--verbose