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lumping together missing optional messages? #174

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nsheff opened this issue Apr 24, 2019 · 1 comment
Closed

lumping together missing optional messages? #174

nsheff opened this issue Apr 24, 2019 · 1 comment
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enhancement likely-solved messaging
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1.2.0

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@nsheff
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nsheff commented Apr 24, 2019 •
edited

for pipelines with many optional arguments that are not included, there are lots of printlines; should we lump these?

## [13 of 15] Sample_13 (ATAC)
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'read2' for option '--input2'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'peak_caller' for option '--peak-caller'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'FRIP_ref' for option '--frip-ref-peaks'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'prealignments' for option '--prealignments'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'deduplicator' for option '--deduplicator'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'trimmer' for option '--trimmer'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'macs_genome_size' for option '--genome-size'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'anno_name' for option '--anno-name'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'TSS_name' for option '--TSS-name'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'keep' for option '--keep'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'no_fifo' for option '--noFIFO'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'lite' for option '--lite'
Writing script to /sfs/lustre/allocations/shefflab/processed/GSE129383/submission/pepatac.py_Sample_13.sub
Job script (n=1; 8.94 Gb): /sfs/lustre/allocations/shefflab/processed//GSE129383/submission/pepatac.py_Sample_13.sub
Dry run, not submitted
## [14 of 15] Sample_14 (ATAC)
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'read2' for option '--input2'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'peak_caller' for option '--peak-caller'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'FRIP_ref' for option '--frip-ref-peaks'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'prealignments' for option '--prealignments'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'deduplicator' for option '--deduplicator'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'trimmer' for option '--trimmer'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'macs_genome_size' for option '--genome-size'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'anno_name' for option '--anno-name'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'TSS_name' for option '--TSS-name'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'keep' for option '--keep'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'no_fifo' for option '--noFIFO'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'lite' for option '--lite'
Writing script to /sfs/lustre/allocations/shefflab/processed/GSE129383/submission/pepatac.py_Sample_14.sub
Job script (n=1; 6.94 Gb): /sfs/lustre/allocations/shefflab/processed//GSE129383/submission/pepatac.py_Sample_14.sub
Dry run, not submitted
## [15 of 15] Sample_15 (ATAC)
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'read2' for option '--input2'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'peak_caller' for option '--peak-caller'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'FRIP_ref' for option '--frip-ref-peaks'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'prealignments' for option '--prealignments'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'deduplicator' for option '--deduplicator'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'trimmer' for option '--trimmer'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'macs_genome_size' for option '--genome-size'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'anno_name' for option '--anno-name'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'TSS_name' for option '--TSS-name'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'keep' for option '--keep'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'no_fifo' for option '--noFIFO'
> Note (missing optional attribute): 'pepatac.py' requests sample attribute 'lite' for option '--lite'
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vreuter commented Apr 24, 2019

Yes

@vreuter vreuter added this to the 0.12 milestone Apr 24, 2019
@vreuter vreuter removed this from the 0.12 milestone May 2, 2019
@nsheff nsheff self-assigned this Jul 19, 2019
nsheff added a commit that referenced this issue Jul 19, 2019
@nsheff
Reduce verbosity of missing options. See #174
7acfc8d
@nsheff nsheff added this to the 0.13 milestone Jan 28, 2020
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