Syntax updates#540
Closed
leandrotiburske wants to merge 268 commits into
Closed
Conversation
Update of nfdata branch with changes from nf-core development version
Dimensionality reduction
* Modify file name * Optional output for handling the absence of VDJ data * Added options to handle the absence of VDJ data * Added options to handle the absence of VDJ data * Create a dummy file when VDJ data are absent * Added output file as optional * Remove CITE-seq Harmony integration * Added sample_type option when reading samplesheet * Remove filtered channels from subworflow * Added dummy file as input to convert.py * Change output name * Added option to handle the absence of CITE-seq data * Added cellannotation module * Change output name * Added atac seq mosality to MuData object * Added doublets and quality filtering for atac * Added variable for ADT and modify string to detect mitho genes * Added folder to save clustering and clustree * Added configuration for CELLRANGERARC_COUNT, added options for retries/errors * Added atac modality to MuData object * Extract channel with filtered matrix * Change process label * Added options to start the pipeline from count matrices * Added ATAC seq filtering to subworkflow * Added options to start from count matrix * Added atac-seq to MuData * Added atac-seq to dimensionality reduction * modify clustering resolution * Added atac-seq modality * Added differential analysis * Added cell annotation * Added cell annotation * Added quality metrics for atac * Doublets for atac * Change clustes parameter * Change cluster parameter * Added atac to mofa integration * Modify space * Added skipping of doublets * Change process label * Added the option to skip doublet detection * Extract channel with h5ad after cellbender * Added option to skip doublet * Added marker gene for sample * Added computation of MAD to label cells of good/bad quality * Added output name * Added module for differential analysis * Added parameters to skip doublet, to start from count matrix, * Modify filters * Added options for demultiplexing and doublets * Added options for demultiplexing and doublets * Added summary on quality control * Added params for demultiplexing * Modify function to read celltypist model * Change resources for the process * Modify output file * Cell annotation post normalization * Added number of cells per donor * Added ouput file * Change output name * Change parameters * WIP: working code before major changes on ATAC part * Added pca plot * Added pca plot * Fix small issue * Fix issue * Fix some issues --------- Co-authored-by: Sara Terzoli <sara.terzoli@fht.org>
* Comment some codes that are specific * Implementation of ATAC subworkflow * Cahnges related to implementation of ATAC subworkflow * Changes parameters on integration * Added options to handle different models * Remove atac modality from mudata * Added cell annotation for peak calling * Added cell cycle * Added atac modality to mofa integration * Implement quality filters for atac * Change parameters for peak calling * Added cell cycle step * Added atac to mofa integration * Added parameters for atac, cell cycle * Added batch correction for atac * Change modules position * Added parameters for filtering * added cellranger parameter * Modify parameter for mudata creation * Change position for blacklist region * Fix the issue when ATAC preprocessing is not invoked * Fix the issue when ATAC preprocessing is not invoked.
* Update protocol documentation * Prettier * Add ruff to pre-commit checks * Don't format modules and subworkflows * Update CHANGELOG * Template update for nf-core/tools version 3.2.1 * update modules with nf-core tools * update cellranger nf-test * update cellranger multi nf-test snaps * update changelog * add TENX_DISABLE_TELEMETRY export to cellranger/multi * Remove ineffective igenomes requests * Make igenomes work properly for FASTA and GTF * Remove multiQC artifact * Update changelog * Update ci.yml * Template update for nf-core/tools version 3.3.1 * Template update for nf-core/tools version 3.3.2 * Add the `accelerator` process directive to the `process_gpu` label configs Add the `accelerator` process directive to the `process_gpu` label configs * if condition on MultiQC step If condition based on if params.skip_multiqc is false, only then run the multiqc step in the workflow * added if condition for multiQC in pipeline completion main block * added if conditions on multiqc report channels * removed = operator in pipeline completion inputs 'multiqc_report=' not required in supplying inputs for Pipiline_Completion() step * update cellranger multi module with nf-core tool * include ocm ids parsing in pipeline * correct parsed ocm barcodes samplesheet * update usage documentation regarding `ocm_ids` * update documentation to have CMO/FFPE/OCM examples separated for easier reading * re-order section order * update changelog * apply prettier * add working rat-OCM cellranger multi testing dataset * add OCM cellranger multi nf-test * remove 'combined' from snapshot * move getGenomeAttributes to main.nf and add star_index parameter * readd getGenomeAttribute to utils * delete unused snap * update simpleaf nf-test as new template * correct nf-test profile * remove template nf-test * update cellranger nf-test as template * update cellrangerarc nf-test as new template * took out emit block from skip_mqc condition this was breaking the pipeline when skip_multiqc was not used * Handle everything withing scrnaseq workflow * Update CHANGELOG * update kallisto nf-test as new template * update star nf-test as new template * update cellrangermulti nf-test as template * correct params.outdir * correct nf-tests based on expected linting * ignore "default.nf.test" file * fix trailling whitespace lint * fix nf-test-content lint * update ro-crate with nf-core lint tool * update ignored nf-test files * perform nf-core tooling version bump * correct errors highlighted by nf-core lint release * correct changelog version and add missing information of tempalte update * Update CHANGELOG * change nf-test function so that pipeline version is not encoded * update snaps * exclude conda profile * fixing end of file * removing trailing whitespaces * patching cellbender/removebackground * remove trailing spaces * Add output folders configuration * modify path for blacklist regions * Change output for integration with mofa * Add missing """ * Remove if condition for filtering low quality cells * Change figure parameters * import missing package * print neighbors information * Change figure parameters * trailing-whitespace * remove trailing spaces * remove trailing spaces * Fix names of models * Fix names of genes --------- Co-authored-by: nictru <nictru32@gmail.com> Co-authored-by: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Felipe Marques de Almeida <felipemarques89@gmail.com> Co-authored-by: Stephen Kelly <stevekm@users.noreply.github.com> Co-authored-by: Mridul Chaudhary <47246321+Mridul-Chaudhary@users.noreply.github.com> Co-authored-by: zxBIB Almeida,Felipe (GCBDS) EXTERNAL <felipe.almeida.ext@boehringer-ingelheim.com> Co-authored-by: Leon Hafner <60394289+LeonHafner@users.noreply.github.com> Co-authored-by: Sara Terzoli <sara.terzoli@fht.org>
… filtering cells, change the way to compute hvg
Pseudobulk
Run differential abundance for every resolution
Add cell-cell interaction to main workflow
This PR is against the
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
9 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).