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genomic-medicine-sweden
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tomte
A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient
MIT License
12
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Targeted heterozygosity check for Tomte
#188
Jakob37
closed
4 days ago
0
Calculate hemoglobin percentage
#187
Jakob37
opened
4 days ago
3
Run Peddy as part of Tomte
#186
Jakob37
opened
4 days ago
1
Merge pull request #181 from genomic-medicine-sweden/dev
#185
Lucpen
closed
1 week ago
1
change way of adding variant caller to vcf
#184
Lucpen
closed
1 week ago
3
Remove break from CALL_VARIANTS subworkflow
#183
Lucpen
opened
2 weeks ago
0
fix bug running variant calling gatk and fix dev bug in bcf norm
#182
Lucpen
closed
2 weeks ago
1
Release 3.0.0 - three kings
#181
Lucpen
closed
1 week ago
3
bump to version 3.0.0
#180
Lucpen
closed
2 weeks ago
1
Release 3.0.0
#179
Lucpen
closed
2 weeks ago
1
Add documentation
#178
Lucpen
closed
2 weeks ago
1
Prepare release 3.0.0
#177
Lucpen
closed
4 weeks ago
5
Gene body coverage calculations
#176
Jakob37
closed
1 month ago
2
Questions about post-processing Tomte for Scout
#175
Jakob37
closed
3 weeks ago
3
Fix versions in multiqc and ymls for drop modules
#174
Lucpen
closed
1 month ago
2
In house scripts do not correctly output version
#173
Lucpen
closed
1 month ago
0
make module_to_export_counts_folder
#172
Lucpen
closed
1 month ago
1
Crash in 03_filter_expression_FraseR.R when running with external counts
#171
Jakob37
closed
1 month ago
5
After running successfully, DROP sometimes re-runs if the pipeline is resumed
#170
Lucpen
opened
1 month ago
0
add parameter --skip_variant_calling
#169
Lucpen
closed
1 month ago
1
Sex info to DROP
#168
Jakob37
closed
1 month ago
4
Template update for nf-core/tools version 3.0.2
#167
Lucpen
closed
1 month ago
3
Improve python code
#166
Lucpen
opened
1 month ago
0
Add tests for subworkflows
#165
Lucpen
opened
1 month ago
0
Running with same sample and case name crashes in RENAME_FILES
#164
Jakob37
opened
1 month ago
2
RNA-seq contamination check
#163
Jakob37
opened
1 month ago
3
An option to use DNA-seq variants?
#162
A97paupic
opened
2 months ago
1
Non-HGNC symbols in the hgncSymbol column
#161
Jakob37
closed
2 months ago
6
Sex info for DROP
#160
Jakob37
closed
2 months ago
1
Update vep to 112 and references encode 46
#159
Lucpen
closed
2 months ago
1
Merge pull request #157 from genomic-medicine-sweden/dev
#158
Lucpen
closed
3 months ago
0
Release 2.2.1
#157
Lucpen
closed
3 months ago
1
fixing multiqc
#156
Lucpen
closed
3 months ago
1
Merge pull request #154 from genomic-medicine-sweden/dev
#155
Lucpen
closed
3 months ago
1
Release 2.2.0
#154
Lucpen
closed
3 months ago
1
Prepare release 2.2.0
#153
Lucpen
closed
3 months ago
1
Allow running DROP without reference samples
#152
Jakob37
closed
3 months ago
7
fix bootstrapann input
#151
Lucpen
closed
3 months ago
1
mRNA and rRNA percentages missing from MultiQC output
#150
Jakob37
closed
1 month ago
3
Added possibility to download refs
#149
Lucpen
closed
3 months ago
1
Add switch for variant calling
#148
Lucpen
closed
1 month ago
0
Adds possibility to make drop database
#147
Lucpen
closed
1 month ago
20
ALLELE_SPECIFIC_CALLING:BOOTSTRAPANN restarts on resume
#146
Jakob37
closed
3 months ago
8
Non-ACGTN reference allele
#145
Jakob37
closed
4 months ago
4
Download references
#144
Lucpen
closed
3 months ago
1
Merge pull request #142 from genomic-medicine-sweden/dev
#143
Lucpen
closed
5 months ago
1
Release 2.1.0
#142
Lucpen
closed
5 months ago
1
Prepare release 2.1.0
#141
Lucpen
closed
5 months ago
1
Remove unnecessary tabix
#140
Lucpen
closed
5 months ago
1
SPLICE_COUNTS_DIR using DROP reference data
#139
Jakob37
closed
5 months ago
1
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