refactor: sequencing and signature tools structure

bbglab · Nov 2, 2023 · ddd2d92 · ddd2d92
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diff --git a/docs/Tools/Sequencing_tools/Bedtools.md → docs/Methods/Sequencing/Bedtools.md b/docs/Tools/Sequencing_tools/Bedtools.md → docs/Methods/Sequencing/Bedtools.md
diff --git a/docs/Tools/Sequencing_tools/Bowtie2.md → docs/Methods/Sequencing/Bowtie2.md b/docs/Tools/Sequencing_tools/Bowtie2.md → docs/Methods/Sequencing/Bowtie2.md
diff --git a/docs/Tools/Sequencing_tools/Cutadapt.md → docs/Methods/Sequencing/Cutadapt.md b/docs/Tools/Sequencing_tools/Cutadapt.md → docs/Methods/Sequencing/Cutadapt.md
diff --git a/docs/Tools/Sequencing_tools/Fastqc.md → docs/Methods/Sequencing/Fastqc.md b/docs/Tools/Sequencing_tools/Fastqc.md → docs/Methods/Sequencing/Fastqc.md
diff --git a/docs/Tools/Sequencing_tools/Samtools.md → docs/Methods/Sequencing/Samtools.md b/docs/Tools/Sequencing_tools/Samtools.md → docs/Methods/Sequencing/Samtools.md
diff --git a/docs/Tools/Sequencing_tools/Trimmomatic.md → docs/Methods/Sequencing/Trimmomatic.md b/docs/Tools/Sequencing_tools/Trimmomatic.md → docs/Methods/Sequencing/Trimmomatic.md
diff --git a/...ools/Variant_callers/Hmftools_pipeline.md → ...cing/Variant_callers/Hmftools_pipeline.md b/...ools/Variant_callers/Hmftools_pipeline.md → ...cing/Variant_callers/Hmftools_pipeline.md
diff --git a/...g_tools/Variant_callers/MosaicForecast.md → ...uencing/Variant_callers/MosaicForecast.md b/...g_tools/Variant_callers/MosaicForecast.md → ...uencing/Variant_callers/MosaicForecast.md
diff --git a/...quencing_tools/Variant_callers/Mutect2.md → ...ods/Sequencing/Variant_callers/Mutect2.md b/...quencing_tools/Variant_callers/Mutect2.md → ...ods/Sequencing/Variant_callers/Mutect2.md
diff --git a/...uencing_tools/Variant_callers/Platinum.md → ...ds/Sequencing/Variant_callers/Platinum.md b/...uencing_tools/Variant_callers/Platinum.md → ...ds/Sequencing/Variant_callers/Platinum.md
diff --git a/...Sequencing_tools/Variant_callers/Sarek.md → ...thods/Sequencing/Variant_callers/Sarek.md b/...Sequencing_tools/Variant_callers/Sarek.md → ...thods/Sequencing/Variant_callers/Sarek.md
diff --git a/docs/Tools/Sequencing_tools/Vep.md → docs/Methods/Sequencing/Vep.md b/docs/Tools/Sequencing_tools/Vep.md → docs/Methods/Sequencing/Vep.md
diff --git a/docs/Tools/Sequencing_tools/pysam.md → docs/Methods/Sequencing/pysam.md b/docs/Tools/Sequencing_tools/pysam.md → docs/Methods/Sequencing/pysam.md
diff --git a/...cing_tools/singleCell/ArchR_scATAC-seq.md → ...Sequencing/singleCell/ArchR_scATAC-seq.md b/...cing_tools/singleCell/ArchR_scATAC-seq.md → ...Sequencing/singleCell/ArchR_scATAC-seq.md
diff --git a/...Sequencing_tools/singleCell/CellRanger.md → ...thods/Sequencing/singleCell/CellRanger.md b/...Sequencing_tools/singleCell/CellRanger.md → ...thods/Sequencing/singleCell/CellRanger.md
diff --git a/...ols/Sequencing_tools/singleCell/Mosaic.md → docs/Methods/Sequencing/singleCell/Mosaic.md b/...ols/Sequencing_tools/singleCell/Mosaic.md → docs/Methods/Sequencing/singleCell/Mosaic.md
diff --git a/...cing_tools/singleCell/Seurat_scRNA_seq.md → ...Sequencing/singleCell/Seurat_scRNA_seq.md b/...cing_tools/singleCell/Seurat_scRNA_seq.md → ...Sequencing/singleCell/Seurat_scRNA_seq.md
diff --git a/...cing_tools/singleCell/Tapestri_insight.md → ...Sequencing/singleCell/Tapestri_insight.md b/...cing_tools/singleCell/Tapestri_insight.md → ...Sequencing/singleCell/Tapestri_insight.md
diff --git a/...ing_tools/singleCell/Tapestri_pipeline.md → ...equencing/singleCell/Tapestri_pipeline.md b/...ing_tools/singleCell/Tapestri_pipeline.md → ...equencing/singleCell/Tapestri_pipeline.md
diff --git a/.../Tools/Signature_tools/DeconstructSigs.md → docs/Methods/Signature/DeconstructSigs.md b/.../Tools/Signature_tools/DeconstructSigs.md → docs/Methods/Signature/DeconstructSigs.md
diff --git a/docs/Tools/Signature_tools/SigProfiler.md → docs/Methods/Signature/SigProfiler.md b/docs/Tools/Signature_tools/SigProfiler.md → docs/Methods/Signature/SigProfiler.md
diff --git a/...Tools/Signature_tools/SigProfilerJulia.md → docs/Methods/Signature/SigProfilerJulia.md b/...Tools/Signature_tools/SigProfilerJulia.md → docs/Methods/Signature/SigProfilerJulia.md
diff --git a/.../Signature_tools/TrinucleotideOrdering.md → ...ethods/Signature/TrinucleotideOrdering.md b/.../Signature_tools/TrinucleotideOrdering.md → ...ethods/Signature/TrinucleotideOrdering.md
diff --git a/docs/Tools/Signature_tools/mSigHDP.md → docs/Methods/Signature/mSigHDP.md b/docs/Tools/Signature_tools/mSigHDP.md → docs/Methods/Signature/mSigHDP.md
diff --git a/docs/Tools/Signature_tools/mSignAct.md → docs/Methods/Signature/mSignAct.md b/docs/Tools/Signature_tools/mSignAct.md → docs/Methods/Signature/mSignAct.md
diff --git a/...ools/Sequencing_tools/Bedtools/index.html → site/Methods/Sequencing/Bedtools/index.html b/...ools/Sequencing_tools/Bedtools/index.html → site/Methods/Sequencing/Bedtools/index.html
diff --git a/...Tools/Sequencing_tools/Bowtie2/index.html → site/Methods/Sequencing/Bowtie2/index.html b/...Tools/Sequencing_tools/Bowtie2/index.html → site/Methods/Sequencing/Bowtie2/index.html
diff --git a/...ools/Sequencing_tools/Cutadapt/index.html → site/Methods/Sequencing/Cutadapt/index.html b/...ools/Sequencing_tools/Cutadapt/index.html → site/Methods/Sequencing/Cutadapt/index.html
diff --git a/.../Tools/Sequencing_tools/Fastqc/index.html → site/Methods/Sequencing/Fastqc/index.html b/.../Tools/Sequencing_tools/Fastqc/index.html → site/Methods/Sequencing/Fastqc/index.html
diff --git a/...ools/Sequencing_tools/Samtools/index.html → site/Methods/Sequencing/Samtools/index.html b/...ools/Sequencing_tools/Samtools/index.html → site/Methods/Sequencing/Samtools/index.html
diff --git a/...s/Sequencing_tools/Trimmomatic/index.html → ...Methods/Sequencing/Trimmomatic/index.html b/...s/Sequencing_tools/Trimmomatic/index.html → ...Methods/Sequencing/Trimmomatic/index.html
diff --git a/...Variant_callers/MosaicForecast/index.html → ...Variant_callers/MosaicForecast/index.html b/...Variant_callers/MosaicForecast/index.html → ...Variant_callers/MosaicForecast/index.html
diff --git a/..._tools/Variant_callers/Mutect2/index.html → ...encing/Variant_callers/Mutect2/index.html b/..._tools/Variant_callers/Mutect2/index.html → ...encing/Variant_callers/Mutect2/index.html
diff --git a/...tools/Variant_callers/Platinum/index.html → ...ncing/Variant_callers/Platinum/index.html b/...tools/Variant_callers/Platinum/index.html → ...ncing/Variant_callers/Platinum/index.html
diff --git a/...ng_tools/Variant_callers/Sarek/index.html → ...quencing/Variant_callers/Sarek/index.html b/...ng_tools/Variant_callers/Sarek/index.html → ...quencing/Variant_callers/Sarek/index.html
diff --git a/site/Tools/Sequencing_tools/Vep/index.html → site/Methods/Sequencing/Vep/index.html b/site/Tools/Sequencing_tools/Vep/index.html → site/Methods/Sequencing/Vep/index.html
diff --git a/site/Tools/Sequencing_tools/pysam/index.html → site/Methods/Sequencing/pysam/index.html b/site/Tools/Sequencing_tools/pysam/index.html → site/Methods/Sequencing/pysam/index.html
diff --git a/...ignature_tools/DeconstructSigs/index.html → ...hods/Signature/DeconstructSigs/index.html b/...ignature_tools/DeconstructSigs/index.html → ...hods/Signature/DeconstructSigs/index.html
diff --git a/...ls/Signature_tools/SigProfiler/index.html → .../Methods/Signature/SigProfiler/index.html b/...ls/Signature_tools/SigProfiler/index.html → .../Methods/Signature/SigProfiler/index.html
diff --git a/...gnature_tools/SigProfilerJulia/index.html → ...ods/Signature/SigProfilerJulia/index.html b/...gnature_tools/SigProfilerJulia/index.html → ...ods/Signature/SigProfilerJulia/index.html
diff --git a/.../Tools/Signature_tools/mSigHDP/index.html → site/Methods/Signature/mSigHDP/index.html b/.../Tools/Signature_tools/mSigHDP/index.html → site/Methods/Signature/mSigHDP/index.html
diff --git a/...Tools/Signature_tools/mSignAct/index.html → site/Methods/Signature/mSignAct/index.html b/...Tools/Signature_tools/mSignAct/index.html → site/Methods/Signature/mSignAct/index.html