- Mar 19, 2020
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Alex Kanitz authored
Rhea naming Closes #94 See merge request zavolan_group/pipelines/rhea!51
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- Mar 18, 2020
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Alex Kanitz authored
Fix log file names Closes #96 See merge request zavolan_group/pipelines/rhea!48
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- Mar 17, 2020
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Alex Kanitz authored
Update cluster.json See merge request zavolan_group/pipelines/rnaseqpipeline!47
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Alex Kanitz authored
Changed adapter trimming parameters to fix overtrimming issues Closes #92 See merge request zavolan_group/pipelines/rnaseqpipeline!46
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- Mar 13, 2020
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BIOPZ-Gypas Foivos authored
fixed snakemake subworkflow typos/bugs Closes #84 See merge request zavolan_group/pipelines/rnaseqpipeline!45
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BIOPZ-Katsantoni Maria authored
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Alex Kanitz authored
Documentation of pipeline steps Closes #60 and #57 See merge request zavolan_group/pipelines/rnaseqpipeline!44
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fixed typos
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CJHerrmann authored
updated pipeline documentation described seqmode specific rules adapted to updates in Snakefile moved star_rpm and samtools index to main snakefile description linked README in documentation and vice versa
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- Mar 12, 2020
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Alex Kanitz authored
add TIN score merge and plot steps See merge request zavolan_group/pipelines/rnaseqpipeline!43
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BIOPZ-Bak Maciej authored
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BIOPZ-Bak Maciej authored
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BIOPZ-Bak Maciej authored
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BIOPZ-Gypas Foivos authored
Alfa integration See merge request zavolan_group/pipelines/rnaseqpipeline!41
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Dominik Burri authored
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Dominik Burri authored
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Dominik Burri authored
moved input_files into top-layer test directory for consistency. corrected removal of test files
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Dominik Burri authored
corrected md5sum for config.yaml remove unnecessary file
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Dominik Burri authored
- renaming bedgraph - creating ALFA qc plots removed conda dependence, moved import statement. included ALFA in finish rule, corrected annotation.gtf and config.yaml, created new .svg
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- Mar 07, 2020
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Alex Kanitz authored
Simplify star_rpm & index_genomic_alignment_samtools. See merge request zavolan_group/pipelines/rnaseqpipeline!38
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- Mar 06, 2020
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BIOPZ-Gypas Foivos authored
Merged paired end and single end rules for star_rpm and index_genomic_alignment_samtools. Fixed wiring of calculate tin score: bam should be input and not params.
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BIOPZ-Gypas Foivos authored
Replace cufflinks image with gffread image Closes #85 See merge request zavolan_group/pipelines/rnaseqpipeline!37
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BIOPZ-Gypas Foivos authored
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BIOPZ-Gypas Foivos authored
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BIOPZ-Gypas Foivos authored
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BIOPZ-Gypas Foivos authored
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- Feb 24, 2020
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Alex Kanitz authored
Generate gene and transcript count tables from salmon Closes #51 See merge request zavolan_group/pipelines/rnaseqpipeline!33
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- compile Salmon gene and transcript count summary tables across all samples in workflow run - add `pandas` to `install/environment.dev.yml` - update rule graph and DAG images
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- Feb 21, 2020
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Alex Kanitz authored
Use minified docker images Closes #67 See merge request zavolan_group/pipelines/rnaseqpipeline!32
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Alex Kanitz authored
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Alex Kanitz authored
Rule to collect all TPM values from Salmon added See merge request zavolan_group/pipelines/rnaseqpipeline!30
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- Remove files with non-deterministic output from `tests/test_integration_workflow/expected_output.files` - Update MD5 sums in `tests/test_integration_workflow/expected_output.md5` - Update new workflow DAG and rule graph images
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Alex Kanitz authored
Handle polyA processing in input preparation script Closes #37 See merge request zavolan_group/pipelines/rnaseqpipeline!31
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