- Aug 20, 2021
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- Jul 14, 2021
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- Apr 15, 2021
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- Mar 25, 2021
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and are therefore not required in the rules. - Snakefile star_rpm: --outWigNorm (default RPM was used) star_rpm: --outWigStrand (default Stranded was used) rename_star_rpm_for_alfa: orientation in params is redundant (Fixes #152) - single_end.snakefile.smk map_genome_star: outFilterMismatchNoverLmax map_genome_star: outFilterScoreMinOverLread map_genome_star: outFilterMatchNminOverLread quantification_salmon: --writeUnmappedNames - paired_end.snakefile.smk pe_map_genome_star: outFilterMismatchNoverLmax pe_map_genome_star: outFilterScoreMinOverLread pe_map_genome_star: outFilterMatchNminOverLread quantification_salmon: --writeUnmappedNames
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- Feb 11, 2021
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- Oct 16, 2020
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BIOPZ-Gypas Foivos authored
- Delete unused files scripts/fg_extract_transcripts.py, scripts/heatmap_and_clustermap.py, scripts/perform_PCA.py - Add rules (pca_kallisto, pca_salmon) that run zpca (https://github.com/zavolanlab/zpca) on genes and transcripts TPM tables from kallisto and salmon. - The output is wired to multiqc_report but the plots are not visualized to multiqc. Update documentation. - Update dag and rulegraph. Fixes #140 #142
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- Jun 23, 2020
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The rules rely on https://github.com/zavolanlab/merge_kallisto Update info in pipeline_documentation.md
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- Jun 12, 2020
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Alex Kanitz authored
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- Apr 28, 2020
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Alex Kanitz authored
- add linked ToC - add table of third party software - add rule graph - clean up sample table description - formalize structure for each rule description - cross-reference rules via inputs/outputs - clean list of references
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- Apr 27, 2020
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- Mar 25, 2020
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- Mar 20, 2020
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BIOPZ-Katsantoni Maria authored
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In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt depending on which is the sense or antisense mate the appropriate variable is populated and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.
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- Mar 19, 2020
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- Mar 13, 2020
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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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