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databio
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peppro
A modular, containerized pipeline for PRO-seq data processing
http://peppro.databio.org/
BSD 2-Clause "Simplified" License
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bulker manifest
#48
nsheff
closed
4 years ago
1
Major updates to pipeline use
#47
jpsmith5
closed
4 years ago
0
chrom_sizes is not an asset
#46
eugeneke-bioinf
closed
4 years ago
4
new way to check assets
#45
nsheff
closed
4 years ago
5
tss enrichment score
#44
mjg54
closed
4 years ago
0
default gro-seq adapters
#43
nsheff
closed
4 years ago
2
summarizer doesn't work when umi_len is 0
#42
nsheff
closed
5 years ago
0
Remove UMI processing with fastp, without adapter removal
#41
nsheff
closed
4 years ago
0
mrna contamination plot to histogram
#40
nsheff
closed
4 years ago
1
UnboundLocalError: local variable 'trim_cmd1' referenced before assignment
#39
nsheff
closed
5 years ago
0
cutadapt_report should not need to be defined in 2 locations
#38
nsheff
opened
5 years ago
1
determining maximum read length should happen in a follow function
#37
nsheff
closed
4 years ago
0
duplicated fastq processing code
#36
nsheff
closed
4 years ago
2
What does 'coverage' do?
#35
nsheff
closed
4 years ago
2
Should we remove individual asset arguments?
#34
nsheff
opened
5 years ago
1
Rename 'adapter' argument?
#33
nsheff
closed
4 years ago
1
Rename complexity argument?
#32
nsheff
closed
4 years ago
0
standardize outputs and folders for removing adapters
#31
nsheff
closed
5 years ago
1
fastqc_folder, fastp results and `QC_hg38`
#30
nsheff
closed
4 years ago
0
code duplication question
#29
nsheff
closed
4 years ago
1
subprocess.CalledProcessError: returned non-zero exit status 2
#28
nsheff
closed
5 years ago
3
zip outputs
#27
nsheff
closed
4 years ago
1
cutadapt output not getting saved for umi_len 0, single end
#26
nsheff
closed
5 years ago
3
simplify _process_fastq
#25
nsheff
closed
4 years ago
4
_process_fastq can return 1 or 2 things
#24
nsheff
closed
4 years ago
2
UnboundLocalError: local variable 'unmap_fq1_dups' referenced before assignment
#22
nsheff
closed
5 years ago
8
name of `--umi` argument
#21
nsheff
closed
5 years ago
3
IndexError: list index out of range. dedup_cmd is blank
#20
nsheff
closed
4 years ago
6
summarizer appears to require a complete project
#19
nsheff
closed
4 years ago
2
update outputs in pipeline interface
#18
nsheff
closed
4 years ago
1
summarizer error
#17
nsheff
closed
5 years ago
1
summarize error with CODE env var
#16
nsheff
closed
5 years ago
1
optigrab
#15
nsheff
opened
5 years ago
5
bowtie2 error results are not logged to primary log
#14
nsheff
closed
4 years ago
3
Setting attmap values doesn't preserve data types
#13
nsheff
closed
4 years ago
9
AttributeError: 'NoneType' object has no attribute 'replace'
#12
nsheff
closed
5 years ago
2
make requirements explicit
#11
nsheff
closed
5 years ago
1
Error: Unable to access jarfile picard
#10
nsheff
closed
5 years ago
6
put master direct updates back into dev
#9
nsheff
closed
5 years ago
0
required checks
#8
nsheff
closed
5 years ago
3
Error: missing fasta file
#7
nsheff
closed
5 years ago
4
fastq_pair
#6
nsheff
closed
5 years ago
1
reports missing
#5
nsheff
closed
4 years ago
1
remove env variables from example
#4
nsheff
closed
5 years ago
0
Installing PEPPRO on Rivanna
#3
ccrobertson
closed
4 years ago
7
Update refgenie docs
#2
nsheff
closed
5 years ago
2
numpy version incompatibility
#23
nsheff
closed
4 years ago
4
when to make peppro public?
#1
nsheff
closed
5 years ago
1
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