percyfal snakemake-rules issues

percyfal / snakemake-rules

Library of snakemake rules.

http://percyfal.github.io/snakemake-rules

MIT License

12 stars 3 forks source link

issues

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Add schema definitions

#53 percyfal opened 6 years ago
0
Rename all rule files to use smk suffix

#52 percyfal closed 6 years ago
0
Update rules to use attempt flag

#51 percyfal opened 7 years ago
0
Samtools sort needs unique temporary file names

#50 percyfal closed 6 years ago
0
Rewrite rules to make use of --restart-times flag

#49 percyfal opened 7 years ago
0
Pass threads to bowtie2-build command

#48 percyfal opened 7 years ago
0
Add rule for samtools idxstats

#47 percyfal opened 7 years ago
0
Make gatk access java_mem per rule

#46 percyfal opened 7 years ago
0
Make picard rules access java_mem per rule

#45 percyfal opened 7 years ago
0
Make one aggregate function

#44 percyfal closed 7 years ago
1
Add outputs to qualimap

#43 percyfal closed 6 years ago
0
Add malt application

#42 percyfal closed 6 years ago
0
Add sga application

#41 percyfal closed 7 years ago
0
Deprecate rule tests not based on pytest_ngsfixtures

#40 percyfal opened 7 years ago
2
Add gatk varianttotable

#39 percyfal closed 6 years ago
0
Add rule for rstudio bookdown documents

#38 percyfal closed 6 years ago
0
Make all gatk vcf rules use vcf.gz

#37 percyfal closed 7 years ago
0
Make tests depend on pytest_ngsfixtures

#36 percyfal closed 7 years ago
1
Put rules in rules directory, code in core

#35 percyfal closed 7 years ago
1
Increase java memory with increasing number of threads

#34 percyfal closed 6 years ago
0
Save run command in tests

#33 percyfal closed 7 years ago
1
mapdamage rule often, not always, throws DuplicateOutput error

#32 percyfal opened 7 years ago
0
Deprecate tophat2

#31 percyfal opened 7 years ago
0
Add configuration option to exclude samples

#30 percyfal closed 7 years ago
2
Add options to syncrules

#29 percyfal closed 7 years ago
0
Add versions to conda env files

#28 percyfal closed 7 years ago
0
Add small workflow tests

#27 percyfal closed 7 years ago
0
Update docs for 0.1

#26 percyfal closed 7 years ago
1
Use multi-scaffold reference

#25 percyfal closed 7 years ago
0
Sort out tuxedo rules

#24 percyfal closed 7 years ago
1
Atomize sratools rules

#23 percyfal opened 7 years ago
0
Add conda recipe

#22 percyfal closed 7 years ago
0
Deprecate label option for picard merge

#21 percyfal closed 7 years ago
0
Add threads and runtime config for all rules

#20 percyfal closed 7 years ago
0
Feature/0.1 beta.6

#19 percyfal closed 8 years ago
0
Rewrite pytest config to include fixtures

#18 percyfal closed 8 years ago
0
Add template generator for EMBOSS and ucsc

#17 percyfal opened 8 years ago
0
Discard app.rules file in favour of app.settings and promote atomic imports

#16 percyfal closed 8 years ago
0
Flatten directory structure to resemble bioconda

#15 percyfal closed 8 years ago
0
Adds single end cutadapt rule

#14 jfear closed 8 years ago
2
Deprecate use of python2 activation command

#13 percyfal closed 8 years ago
0
bamtools filter script does not resolve {{input.script}}

#12 percyfal closed 8 years ago
0
Add ucsc rule genePredToBed

#11 percyfal closed 8 years ago
0
Rename star_align to star_align_pe

#10 percyfal closed 8 years ago
0
Throw error if unsupported annotation format provided to rpkmforgenes

#9 percyfal opened 8 years ago
1
Add option use_multimapped for rnaseq applications

#8 percyfal closed 8 years ago
0
If STAR reference is transcriptome rule should remove soft-clipping and gaps for use with e.g. RSEM

#7 percyfal closed 8 years ago
1
initalize_input returns too many samples if common prefix

#6 percyfal closed 8 years ago
1
Add test data set

#5 percyfal closed 8 years ago
0
Make separate rules for metrics output

#4 percyfal opened 8 years ago
0