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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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Reduce verbosity of missing options. See #174
7acfc8d
nsheff
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for pipelines with many optional arguments that are not included, there are lots of printlines; should we lump these?
The text was updated successfully, but these errors were encountered: