bihealth digestiflow-demux issues

bihealth / digestiflow-demux

:spaghetti: Digestiflow Demultiplexing Tool

MIT License

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issues

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Project structure

#42 messersc opened 2 years ago
1
Make it possible to only write out Samplesheets without running snakemake afterwards

#41 messersc opened 2 years ago
0
Phase out DRMAA

#40 messersc opened 2 years ago
0
Implement new sample sheet writer for bclconvert

#39 messersc opened 2 years ago
1
Add tests for get_result_files_demux function used by Snakemake.

#38 messersc closed 2 years ago
0
Fix missing s.locs files in the TARballs

#37 martenj opened 2 years ago
0
fix failed BCL generation without SampleSheet

#36 martenj closed 2 years ago
0
Cleanup conda environments

#35 messersc opened 2 years ago
2
Investigate how to continue demux runs if fastqc or multiqc should fail

#34 messersc opened 2 years ago
0
Investigate Illumina's BCLConvert

#33 messersc opened 2 years ago
4
BaseMaskConfigException: You cannot assign UMIs ('M') if using bcl2fastq

#32 messersc opened 2 years ago
0
Allow Snakemake workflow to use Singularity images

#31 holtgrewe opened 3 years ago
0
Use ZIP for the demux HTML reports

#30 holtgrewe opened 4 years ago
0
Option for no lane splitting

#29 holtgrewe opened 4 years ago
0
Issue with too many files in multiqc

#28 holtgrewe opened 4 years ago
0
Create folder with project name in output

#27 holtgrewe opened 4 years ago
1
Only pickup flow cell folders for read flow cells

#26 holtgrewe opened 4 years ago
0
cellranger mkfastq support?

#25 tgjohnst opened 4 years ago
1
Properly catch bases mask differences

#24 holtgrewe opened 5 years ago
0
Refuse demultiplexing if sheet is empty

#23 holtgrewe closed 4 years ago
0
Add dependency drmaa to conda recipe

#22 holtgrewe closed 4 years ago
1
Store generated HTML report with output

#21 holtgrewe closed 5 years ago
0
Tarball creation and other fixes.

#20 holtgrewe closed 5 years ago
0
Ignore libraries without configured lanes.

#19 messersc closed 5 years ago
1
discard samples that do not have a lane in config

#18 messersc closed 5 years ago
0
Remove old sample sheets before running workflow.

#17 messersc closed 5 years ago
0
Remove sample sheets in output directories before launching Snakemake

#16 messersc closed 5 years ago
0
Feature/new server params

#15 messersc closed 5 years ago
4
Add parameter to keep even qc failed reads

#14 holtgrewe closed 5 years ago
3
WIP: Fix number of template reads,

#13 messersc closed 5 years ago
0
Unindexed runs do not produce Undetermined.fastq.gz, but snakemake expects them

#12 messersc closed 5 years ago
2
bcl2fastq2: set --minimum-trimmed-read-length dependent on bases mask?

#11 messersc closed 5 years ago
1
snakemake_support.py does not handle R3, R4

#10 messersc closed 5 years ago
0
Feature/per sample bases mask

#9 messersc closed 5 years ago
0
Add support for index pools, e.g. from 10x.

#8 messersc closed 5 years ago
1
Add capability to parse and check user-given bases mask (demux_reads …

#7 messersc closed 5 years ago
7
Enable use of bcl2fastq packages from conda.

#6 messersc closed 5 years ago
1
Use anaconda packages

#5 holtgrewe closed 5 years ago
0
Support for per-library (or lane) bases masks

#4 holtgrewe closed 5 years ago
2
Support for UMIs

#3 holtgrewe closed 5 years ago
1
Handling of runs with UMIs

#2 messersc closed 5 years ago
2
Add support for picard demultiplexing

#1 messersc closed 5 years ago
2