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Commits on Feb 28, 2024

• Make BBSPLIT indexing behave itself (nf-core#5005)

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Commits on Feb 26, 2024

• Fix sortmerna indexing (nf-core#5003)

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• Allow sortmerna to operate in indexing-only mode (nf-core#4998)

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Commits on Feb 24, 2024

• Reorder rnaseq preprocessing, fix minor issues, test sortmerna (nf-core#4982)

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Commits on Feb 21, 2024

• Fix conda cat version to match container in cat/fastq (nf-core#4965)

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• Stop UMItools prepare-for-rsem command writing to the input file (nf-core#4966)

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Commits on Feb 19, 2024

• Tidy up new bits of fastq_align_star (nf-core#4939)

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Commits on Feb 16, 2024

• Update fastq_align_star for nf-test and handle transcriptome alignment better (nf-core#4927)

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• Bump umi tools (nf-core#4932)

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Commits on Feb 14, 2024

• tximport doesn't do anything with coldata (nf-core#4908)

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Commits on Feb 13, 2024

• Umitools prepareforrsem (nf-core#4897)

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• Migrate Summarizedexperiment module from rnaseq workflow (nf-core#4890)

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Commits on Feb 8, 2024

• Add tximport module (port from rnaseq) (nf-core#4884)

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Commits on Feb 7, 2024

• Restore input format of tx2gene, allow for lack of prefix (nf-core#4869)

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Commits on Feb 6, 2024

• Add tx2gene module (formerly local to rnaseq) (nf-core#4854)

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Commits on Feb 2, 2024

• Fix some linting issues in rnaseq_preprocessing workflow (nf-core#4836)

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Commits on Feb 1, 2024

• Uniqify some test names to please nf-test 0.8.4 (nf-core#4829)

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Commits on Jan 31, 2024

• Add factored-out RNA-seq preprocessing subworkflow (nf-core#4813)

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Commits on Jan 23, 2024

• Updating gffread tests (nf-core#4790)

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Commits on Jan 11, 2024

• Try for stable snapshotting strategy in fastq_subsample_fq_salmon, fastq_download_prefetch_fasterqdump_sratools (nf-core#4714)

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Commits on Jan 8, 2024

• Fix field matching in GSEA cls building (nf-core#4683)

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Commits on Jan 7, 2024

• Bump shinyngs (nf-core#4609)

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Commits on Dec 29, 2023

• Custom/cat additional fasta (delocalise rnaseq module) (nf-core#4636)

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Commits on Dec 14, 2023

• Bump rseqc (nf-core#4601)

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• Deal properly with empty classes in GSEA preparation (nf-core#4600)

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Commits on Dec 5, 2023

• Pull multiqc static multiqc test data (nf-core#4539)

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Commits on Dec 1, 2023

• Update affy_justrma.R to increase download timeout (nf-core#4523)

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Commits on Nov 27, 2023

• DESeq2 and Limma can be a low-resource processes (nf-core#4423)

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Commits on Nov 24, 2023

• Nftest reseqc inferexperiment (nf-core#4397)

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Commits on Nov 23, 2023

• Nftest reseqc innerdistance (nf-core#4399)

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• Add nf-test tests for rseqc/bamstat (nf-core#4392)

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Commits on Nov 22, 2023

• Bake tximport transcript lengths into DESeq2 D/E (nf-core#4376)

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Commits on Nov 15, 2023

• Kallisto quant tidy up (nf-core#4334)

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Commits on Nov 9, 2023

• Kallisto fragment length params to channels, strand to meta (nf-core#4309)

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Commits on Nov 2, 2023

• Fix up kallisto (nf-core#4271)

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