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vanheeringen-lab
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seq2science
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
https://vanheeringen-lab.github.io/seq2science
MIT License
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BUG: [scATAC-seq successful run but bam file and snap object are missing cell barcodes]
#976
inesmarais
closed
1 year ago
6
drop use of sanitized_samples
#975
siebrenf
closed
1 year ago
0
more informative flake
#974
siebrenf
closed
1 year ago
0
Envs2
#973
siebrenf
closed
1 year ago
1
faster envs
#972
siebrenf
closed
1 year ago
3
gp ref
#971
siebrenf
closed
1 year ago
0
update prefetch
#970
siebrenf
closed
1 year ago
0
ASAP to trimmed FASTQs
#969
siebrenf
closed
1 year ago
0
Prioritity
#968
siebrenf
closed
1 year ago
0
Prio
#967
siebrenf
closed
1 year ago
0
clear error, fixes #962
#966
Maarten-vd-Sande
closed
1 year ago
0
doesn't work as grouped jobs are ignored when not submitting to cluster
#965
Maarten-vd-Sande
closed
1 year ago
1
fix custom assemblies in deseq2 scripts
#964
siebrenf
closed
1 year ago
0
WIP: SRA in tmpdir
#963
simonvh
closed
11 months ago
0
BUG: Incorrect SRA files (RNA-seq)
#962
simonvh
closed
1 year ago
1
FR: Use temporary directories for sra and temporary fastq files
#961
simonvh
opened
1 year ago
14
Update salmon.yaml
#960
Maarten-vd-Sande
closed
1 year ago
0
Update bam_cleaning.smk
#959
Maarten-vd-Sande
closed
1 year ago
0
Patch
#958
Maarten-vd-Sande
closed
1 year ago
0
Update scrna_seq.md
#957
Rebecza
closed
1 year ago
0
reanalysis gsm numbers
#956
Maarten-vd-Sande
closed
1 year ago
0
localrules
#955
Maarten-vd-Sande
closed
1 year ago
1
explanation fixed
#954
Maarten-vd-Sande
closed
1 year ago
1
--debug for sra lookup
#953
Maarten-vd-Sande
closed
1 year ago
0
Gsa support
#952
Maarten-vd-Sande
closed
1 year ago
0
Update configuration_logging.smk
#951
Maarten-vd-Sande
closed
1 year ago
0
Update requirements.yaml
#950
Maarten-vd-Sande
closed
1 year ago
2
force assembly hub flag
#949
Maarten-vd-Sande
closed
1 year ago
0
Update configuration_generic.smk
#948
Maarten-vd-Sande
closed
1 year ago
1
update_snakemake
#947
Maarten-vd-Sande
closed
1 year ago
0
Update multiqc.yaml
#946
Maarten-vd-Sande
closed
1 year ago
0
Update configuration_generic.smk
#945
Maarten-vd-Sande
closed
1 year ago
0
Update gimme
#944
Maarten-vd-Sande
closed
1 year ago
1
Update ucsc.yaml
#943
Maarten-vd-Sande
closed
1 year ago
0
BUG: Problem with the Initiation
#942
XimenezJP
closed
1 year ago
6
Q: Stuck with initialisation of a workflow (atac-seq)
#941
WouterVGKULEUVEN
closed
1 year ago
13
update bedtools env; fixes #939
#940
Maarten-vd-Sande
closed
1 year ago
0
Issue with Chip-seq pipeline: jobid: 27: one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!
#939
Jerolen
closed
1 year ago
8
Fluff
#938
Maarten-vd-Sande
closed
1 year ago
0
Revert "Fun fluff"
#937
Maarten-vd-Sande
closed
1 year ago
0
explain tests failing
#936
Maarten-vd-Sande
closed
1 year ago
1
optional motif2factors
#935
Maarten-vd-Sande
closed
1 year ago
0
Fun fluff
#934
Maarten-vd-Sande
closed
1 year ago
1
Update docs
#933
Maarten-vd-Sande
closed
1 year ago
0
Update tximeta.yaml
#932
Maarten-vd-Sande
closed
1 year ago
1
slightly cleaner genomepy error
#931
Maarten-vd-Sande
closed
1 year ago
1
Multiqc reports
#930
Maarten-vd-Sande
closed
1 year ago
2
fix schema for deseq in multiqc
#929
Maarten-vd-Sande
closed
1 year ago
2
Bugfix bioreps
#928
Maarten-vd-Sande
closed
1 year ago
2
Update CHANGELOG.md
#927
Rebecza
closed
1 year ago
1
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