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IARCbioinfo
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needlestack
Multi-sample somatic variant caller
GNU General Public License v3.0
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nextflow no long support DSL1
#194
lxm1117
opened
9 months ago
0
Is 'QUAL' in vcf file the 'QVAL' in the paper?
#193
isshamie
closed
2 years ago
1
`--output_vcf` parameter doesn't work when including a relative path
#192
Fer020707
opened
2 years ago
6
Failed to open file
#191
theo-allnutt-bioinformatics
closed
2 years ago
3
Advice about running on gcs?
#190
njbernstein
opened
3 years ago
1
vagrant + nextflow + docker test run howto
#189
darked89
closed
2 years ago
1
Vagrant, trusty64 and java 8 for the latest nextflow
#188
darked89
closed
4 years ago
1
Preparing next beta
#187
mfoll
closed
5 years ago
0
Update needlestack.nf
#186
pditommaso
closed
5 years ago
0
V1.1b
#185
mfoll
closed
5 years ago
0
Dev
#184
mfoll
closed
5 years ago
0
migrate to CircleCI 2.0
#183
tdelhomme
opened
6 years ago
0
add needlestack logo in log.info
#182
tdelhomme
closed
5 years ago
0
Disambiguation between allelic fraction and allele frequency
#181
chabriera
opened
6 years ago
9
allow nextflow resume to work
#180
mfoll
closed
4 years ago
0
rename output options
#179
mfoll
opened
6 years ago
0
Input in first process missing
#178
luisas
opened
6 years ago
1
PR to create v1.1 release
#177
tdelhomme
closed
6 years ago
1
max_dp default value in readme is wrong
#176
mfoll
closed
5 years ago
0
correct insertion extraction from mpileup
#175
tdelhomme
opened
6 years ago
1
add INFO field containing allelic frequency
#174
tdelhomme
closed
6 years ago
1
rewrite indel output format
#173
tdelhomme
closed
4 years ago
1
PDF name size should be controlled
#172
tdelhomme
closed
4 years ago
4
update java to 1.8 in circleci.yml
#171
tdelhomme
closed
4 years ago
0
Allow BAM index files to be called .bai (not only .bam.bai)
#170
mfoll
closed
4 years ago
0
Replace the input of a BAM directory with a text file listing BAM to include?
#169
mfoll
closed
4 years ago
8
adapt plot option for annotation mode
#168
tdelhomme
closed
6 years ago
0
adapt --plots option to the annotation mode
#167
tdelhomme
closed
4 years ago
0
How to identify each sample?
#166
FerVallejoLec
closed
6 years ago
1
Add extra robust regression parameters
#165
V-Catherine
closed
7 years ago
0
add extra robust regression parameters
#164
V-Catherine
closed
7 years ago
0
piping, perl replaced by c++, alignment plot
#163
mfoll
closed
7 years ago
3
add extra robust regression parameters
#162
tdelhomme
closed
4 years ago
3
--help should exit 0
#161
tdelhomme
closed
7 years ago
0
needlestack.nf --help should exit with 0 not 1
#160
mmterpstra
closed
7 years ago
1
Github readme != Docker readme
#159
mmterpstra
closed
7 years ago
2
Feature: Consider realignment using freebayes/glia/???
#158
mmterpstra
closed
4 years ago
2
Manage bed specification for both bed and region
#157
tdelhomme
closed
7 years ago
0
Test if pairs_file exists and throw an error if not
#156
mfoll
closed
4 years ago
0
improve output VCF header
#155
tdelhomme
opened
7 years ago
0
Consider removing the BAQ option in samtools mpileup
#154
mfoll
opened
7 years ago
0
Multiple tumors should be able to share the same matched normal
#153
mfoll
closed
4 years ago
4
Using renamed symlinks as input BAM files doesn't work with --use_file_name option
#152
mfoll
closed
7 years ago
1
Prepare v1.1b
#151
mfoll
closed
7 years ago
0
V1.0 merge
#150
mfoll
closed
7 years ago
0
Add an option to only plot somatic mutations
#149
mfoll
closed
7 years ago
1
Check that all sample names in the pairs_file file actually exist
#148
mfoll
closed
4 years ago
1
Make the main 3 processes pipe-friendly to avoid intermediate outputs
#147
mfoll
closed
7 years ago
0
Re-write pileup2baseindel.pl in C++
#146
mfoll
closed
7 years ago
0
debug on RG and all AO = 0
#145
tdelhomme
closed
7 years ago
0
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