IARCbioinfo needlestack issues

IARCbioinfo / needlestack

Multi-sample somatic variant caller

GNU General Public License v3.0

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issues

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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