AgResearch gbs_prism issues

AgResearch / gbs_prism

refactored GBS processing

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refactoring 2023_illumina_sequencing_c -> 2024_illumina_sequencing_d

#46 BenjaminJPerry closed 5 months ago
1
port keyfile sanitising to gquery

#45 afmcc opened 8 months ago
1
pipeline should try to keep going after problem with walkin keyfile

#43 afmcc opened 8 months ago
0
Update run_kgd.R

#42 doddsk closed 11 months ago
0
Adding andrewsa, henryh, frenchm, hicklandm to auto-emails

#40 BenjaminJPerry closed 11 months ago
0
adding --interactive to multiqc call in ag_gbs_qc_prism.sh

#39 BenjaminJPerry closed 11 months ago
0
Update SampleStatsRawCombined.csv in run_kgd.R

#38 doddsk closed 1 year ago
0
InbCompare mouse-over

#37 doddsk closed 1 year ago
0
Update run_kgd.R

#36 doddsk closed 1 year ago
0
Another r script which may benefit from set.seed()

#35 BenjaminJPerry closed 1 year ago
0
set.seed() included for pseudorandom number generation

#34 BenjaminJPerry closed 1 year ago
0
added echo answer to read_answer_with_default()

#33 BenjaminJPerry closed 1 year ago
2
allow _ in SampleID in run_kgd.R

#32 doddsk closed 2 years ago
0
KGD narratives

#31 doddsk closed 2 years ago
0
Update make_cohort_pages.py

#30 doddsk closed 2 years ago
1
Update beta binomial fitting & plotting in run_kgd.R

#29 doddsk closed 2 years ago
0
InbCompare.png is using the default “rainbow” palette instead of specified “teal” palette

#28 afmcc closed 2 years ago
2
Update run_kgd.R

#27 doddsk closed 2 years ago
0
automatically add header to sample sheet if missing

#26 afmcc closed 4 years ago
1
delete run fails

#25 afmcc closed 4 years ago
2
keyfile admin for spiked-in GBS

#24 afmcc opened 4 years ago
0
listDBKeyfile.sh - problem with Tassel v5 format

#23 afmcc opened 4 years ago
2
plot label improvement needed

#22 afmcc opened 5 years ago
0
Check hits labelled "N/A" on tax plots - is there more information available that can be displayed?

#21 afmcc opened 5 years ago
0
various plots show solid red line for zero counts (e.g. controls)

#20 afmcc opened 5 years ago
0
uneak picks up sampled fastq in common_sequence sub-folder

#19 afmcc closed 5 years ago
1
process 190723_D00390_0488_ACDR71ANXX

#18 afmcc closed 5 years ago
1
old results imported into yield table

#17 afmcc closed 5 years ago
1
keyfile import did not correctly update fastq locations

#16 afmcc closed 5 years ago
2
add num_threads prompt to run_gbs wrapper (default to 16 or maybe 8)

#15 afmcc opened 5 years ago
0
change order of transactions in keyfile import

#14 afmcc opened 5 years ago
0
intermittent hang of tag sampling

#13 afmcc closed 5 years ago
1
results not imported

#12 afmcc opened 5 years ago
0
headers in generated code causes error messages

#11 afmcc closed 5 years ago
1
modify data_prism so easier to complete and import

#10 afmcc opened 5 years ago
0
database_prism should remove temp files

#9 afmcc opened 5 years ago
0
logging for target=all , needs partitioning into separate logs for each sub-step

#8 afmcc opened 5 years ago
0
bwa_mapping step completes but landmark file not generated

#7 afmcc opened 5 years ago
0
disposition of fastq files from bcl2fastq wrong

#6 afmcc opened 5 years ago
0
need to fix sample sheet handling

#5 afmcc closed 5 years ago
1
unable to remove a temp file created by another user during database import

#4 afmcc opened 5 years ago
0
default output folder created in the wrong place

#3 afmcc opened 5 years ago
0
add a post-import check, for blank fastq_link columns

#2 afmcc opened 5 years ago
2
"delete run" database stored proc needed

#1 afmcc opened 5 years ago
0