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BIMSBbioinfo
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pigx_bsseq
bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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cluster jobs are always sent to queue "all"
#93
katwre
closed
6 years ago
4
Cleanup repo
#92
Blosberg
closed
6 years ago
1
Handle low-coverage case.
#91
Blosberg
closed
6 years ago
1
Cleanup repo
#90
Blosberg
closed
6 years ago
1
separate validation from parsing in `parse_samples`
#89
rekado
opened
6 years ago
3
Check refgenome for pre-existing BS_conv (or writeability)
#88
Blosberg
closed
6 years ago
1
Flag actual warnings from our QC checks
#87
Blosberg
opened
6 years ago
0
pulls chrom. lengths from the same source as for the bigwig files.
#86
Blosberg
closed
6 years ago
0
remove overlap from Extract Methylation Calls figure
#85
Blosberg
closed
6 years ago
2
Make final reports case-dependent
#84
Blosberg
opened
6 years ago
0
Path to source directory and SampleID included in final report. Shoul…
#83
Blosberg
closed
6 years ago
3
*original* input files should be listed in the final report
#82
Blosberg
closed
6 years ago
1
Remove output top-level directory from params section in final report
#81
Blosberg
closed
6 years ago
1
allow non-numeric treatment vectors
#80
Blosberg
closed
4 years ago
2
final report tries to access biocinstaller
#79
rekado
closed
6 years ago
2
Diffmeth opt v2
#78
Blosberg
closed
6 years ago
0
Right now only one round of diffmeth is incorporated into the report
#77
alexg9010
closed
6 years ago
5
Single final report
#76
alexg9010
closed
6 years ago
3
output documentation to pigx_work
#75
Blosberg
closed
6 years ago
1
check write permission of genome reference directory
#74
rekado
closed
6 years ago
2
Remove internet-dependence from overviewplot for annotation of diffmeth
#73
alexg9010
closed
6 years ago
1
omit output-dir from pre-existence check, and confirm unique referen…
#72
Blosberg
closed
6 years ago
0
Fixes issue #42 (changed qvalue to fdr)
#71
katwre
closed
6 years ago
0
bed file reference must be included
#70
Blosberg
closed
6 years ago
7
diffmeth.report.utf8.md does not exist
#69
Blosberg
closed
6 years ago
1
Log file error: "shall be touched but does not exist"
#68
Blosberg
closed
6 years ago
3
snakemake commands prepended with ` set -euo pipefail; `
#67
Blosberg
closed
6 years ago
2
move custom samplesheet parsing code out of driver script
#66
rekado
opened
6 years ago
5
Export bigwig
#65
Blosberg
closed
6 years ago
3
rewrite tool execution strings
#64
rekado
closed
6 years ago
0
investigate "onerror" rules
#63
rekado
closed
6 years ago
1
hoist "--unlock" option
#62
rekado
closed
6 years ago
0
when UNINSTALLED is not set: give a nicer error message
#61
rekado
closed
6 years ago
0
Change report generation from multi-report-merging to single report generation
#60
alexg9010
closed
6 years ago
1
printing targets as part of the "all" rule forces re-execution
#59
rekado
closed
6 years ago
0
make rule names descriptive
#58
Blosberg
closed
6 years ago
0
Need to check for availability of cluster before submission.
#57
Blosberg
closed
6 years ago
0
[during cluster submission]: qstat doesn't show which jobs are currently in execution
#56
Blosberg
closed
6 years ago
0
use subprocess instead of os.system()
#55
rekado
closed
6 years ago
0
All values in Read1 must be unique
#54
rekado
closed
6 years ago
2
Cluster execution fails: file not found
#53
rekado
closed
6 years ago
1
Script to Shell(Run)
#52
alexg9010
closed
6 years ago
6
reports are non-deterministic
#51
rekado
closed
6 years ago
1
DiRs reorganized
#50
Blosberg
closed
6 years ago
1
record R package locations at configure time, recover at runtime
#49
rekado
closed
4 years ago
8
Do not depend on connection to AnnotationHub servers
#48
rekado
closed
6 years ago
2
Add license headers
#47
rekado
closed
6 years ago
0
re-execution being forced.
#46
Blosberg
closed
6 years ago
4
Add command line option to select rules
#45
rekado
closed
6 years ago
0
change cluster notifcations to only error
#44
alexg9010
closed
6 years ago
0
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