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Adding cellrangermulti subworkflow #276

Merged
merged 160 commits into from
May 22, 2024
Merged

Adding cellrangermulti subworkflow #276

merged 160 commits into from
May 22, 2024

Commits on Nov 7, 2023

  1. Add cellranger multi testing assets

    @fmalmeida
    fmalmeida committed Nov 7, 2023
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  2. allow cellrangermulti option

    @fmalmeida
    fmalmeida committed Nov 7, 2023
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  3. include cellrangermulti testing conf/profile

    @fmalmeida
    fmalmeida committed Nov 7, 2023
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  4. allow cellrangermulti option

    @fmalmeida
    fmalmeida committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. fix example samplesheet

    @fmalmeida
    fmalmeida committed Nov 8, 2023
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  2. fixed samplesheet for cellranger multi

    @fmalmeida
    fmalmeida committed Nov 8, 2023
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  3. don't get cellrangemulti metadata if not needed

    @fmalmeida
    fmalmeida committed Nov 8, 2023
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Commits on Nov 9, 2023

  1. fix check_samplesheet script to be more generic

    @fmalmeida
    fmalmeida committed Nov 9, 2023
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  2. update input_check for cellranger multi

    @fmalmeida
    fmalmeida committed Nov 9, 2023
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  3. avoid renaming sample ids in input check

    @fmalmeida
    fmalmeida committed Nov 9, 2023
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  4. generate a parsed input channel for cellrangermulti sub-workflow

    @fmalmeida
    fmalmeida committed Nov 9, 2023
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  5. defined cellrangemulti sub-workflow and parsed input channel for exec… 

    …ution
    @fmalmeida
    fmalmeida committed Nov 9, 2023
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Commits on Nov 10, 2023

  1. included gex (normal) reference building and updated cellranger modules

    @fmalmeida
    fmalmeida committed Nov 10, 2023
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Commits on Nov 13, 2023

  1. include mkvdjref

    @fmalmeida
    fmalmeida committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. refactored sample mapping

    @fmalmeida
    fmalmeida committed Nov 14, 2023
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  2. finally cellranger multi running, with errors, but now can be debugged

    @fmalmeida
    fmalmeida committed Nov 14, 2023
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  3. not finding samples in data directory

    @fmalmeida
    fmalmeida committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. saving quick changes for shifting development workspace

    @fmalmeida
    fmalmeida committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. include option for unzipping reference files

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Nov 16, 2023
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Commits on Nov 17, 2023

  1. First successfull run of cellranger multi with renaming module

    @fmalmeida
    fmalmeida authored and zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Nov 17, 2023
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Commits on Nov 20, 2023

  1. add whiteline

    @fmalmeida
    fmalmeida committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. Testing github traffic

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Nov 21, 2023
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  2. Remove file used for testing

    fmalmeida committed Nov 21, 2023
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Commits on Nov 22, 2023

  1. input dataset parsing refactored and fixed

    fmalmeida committed Nov 22, 2023
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  2. include cellrangermulti outputs in mqc channel

    fmalmeida committed Nov 22, 2023
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Commits on Nov 23, 2023

  1. include option for cellrangermulti in mtx conversion modules

    fmalmeida committed Nov 23, 2023
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  2. add files filter for cellranger multi outputs

    fmalmeida committed Nov 23, 2023
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  3. include cellranger multi outputs to mtx conversion subworkflow

    fmalmeida committed Nov 23, 2023
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  4. update changelog

    fmalmeida committed Nov 23, 2023
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  5. remove unused file

    fmalmeida committed Nov 23, 2023
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  6. update comment

    fmalmeida committed Nov 23, 2023
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  7. remove unused params

    @fmalmeida
    fmalmeida committed Nov 23, 2023
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  8. update nextflow schema

    @fmalmeida
    fmalmeida committed Nov 23, 2023
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Commits on Feb 23, 2024

  1. update version of cellranger multi module

    fmalmeida committed Feb 23, 2024
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  2. delete unnecessary module

    fmalmeida committed Feb 23, 2024
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  3. update modules.config

    fmalmeida committed Feb 23, 2024
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  4. include newly required parameters

    fmalmeida committed Feb 23, 2024
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  5. remove unnecessary module

    fmalmeida committed Feb 23, 2024
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  6. remove unwanted args

    fmalmeida committed Feb 23, 2024
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Commits on Feb 26, 2024

  1. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 247-su… 

    …pport-for-10x-ffpe-scrna
    fmalmeida committed Feb 26, 2024
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  2. add new params

    fmalmeida committed Feb 26, 2024
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  3. update modules due linting

    fmalmeida committed Feb 26, 2024
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  4. include new columns in samplesheet checker

    fmalmeida committed Feb 26, 2024
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  5. add docker image workaround

    fmalmeida committed Feb 26, 2024
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  6. fix linting

    fmalmeida committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. update nextflow schema

    @fmalmeida
    fmalmeida committed Feb 27, 2024
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  2. applied prettier changes

    @fmalmeida
    fmalmeida committed Feb 27, 2024
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  3. make param.fasta and params.gtf optional again

    @fmalmeida
    fmalmeida committed Feb 27, 2024
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Commits on Mar 7, 2024

  1. Merge remote-tracking branch 'origin/dev' into 247-support-for-10x-ff… 

    …pe-scrna
    @grst
    grst committed Mar 7, 2024
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Commits on Mar 11, 2024

  1. update publishDir path

    fmalmeida committed Mar 11, 2024
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  2. Merge branch '247-support-for-10x-ffpe-scrna' of https://github.com/n… 

    …f-core/scrnaseq into 247-support-for-10x-ffpe-scrna
    fmalmeida committed Mar 11, 2024
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Commits on Mar 19, 2024

  1. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 247-su… 

    …pport-for-10x-ffpe-scrna
    @fmalmeida
    fmalmeida committed Mar 19, 2024
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  2. add sample headers to schema

    @fmalmeida
    fmalmeida committed Mar 19, 2024
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  3. add missing modules

    @fmalmeida
    fmalmeida committed Mar 19, 2024
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  4. remove debugging .view()

    @fmalmeida
    fmalmeida committed Mar 19, 2024
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  5. update cellrager/count

    @fmalmeida
    fmalmeida committed Mar 19, 2024
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  6. small dataset cannot run emptydrops

    fmalmeida committed Mar 19, 2024
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  7. also run for cellranger/multi

    fmalmeida committed Mar 19, 2024
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  8. fix white space

    fmalmeida committed Mar 19, 2024
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  9. do not run emptydrops for cellranger arc, and update ch_matrices filt… 

    …er so empty drops only load raw matrices from cellrager, kallisto and star (alevin has only raw).
    fmalmeida committed Mar 19, 2024
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Commits on Mar 20, 2024

  1. add cellrangermulti in aligners options for conversion and add * to m… 

    …atch more generically.
    fmalmeida committed Mar 20, 2024
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  2. parse cellrangermulti matrix outputs to filter between raw / filtered… 

    … results,
    fmalmeida committed Mar 20, 2024
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  3. fixing filtering option and using correct cellranger-multi mtxs

    fmalmeida committed Mar 20, 2024
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  4. add nf-test for cellranger multi

    @fmalmeida
    fmalmeida committed Mar 20, 2024
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  5. also test cellrangermulti

    @fmalmeida
    fmalmeida committed Mar 20, 2024
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Commits on Mar 21, 2024

  1. revert cellranger modules to latest, without the multi-out-channels a… 

    …nd add parser in the local subworkflow to perform the file selection
    fmalmeida committed Mar 21, 2024
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Commits on Mar 25, 2024

  1. update modules to latest version

    fmalmeida committed Mar 25, 2024
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  2. add a parser for raw/filtered results

    fmalmeida committed Mar 25, 2024
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  3. update comment line

    fmalmeida committed Mar 25, 2024
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Commits on Apr 2, 2024

  1. add lint fix

    @fmalmeida
    fmalmeida committed Apr 2, 2024
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  2. fixed with new from template using lint

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    fmalmeida committed Apr 2, 2024
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Commits on Apr 8, 2024

  1. fix changelog.

    @fmalmeida
    fmalmeida committed Apr 8, 2024
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  2. update assets for subworkflow

    fmalmeida committed Apr 8, 2024
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  3. start removing channels related to "deprecated" additional csvs

    fmalmeida committed Apr 8, 2024
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Commits on Apr 10, 2024

  1. fix projectDir

    fmalmeida committed Apr 10, 2024
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  2. add a parser for frna/cmo data from customised, unified, barcodes sam… 

    …plesheet
    fmalmeida committed Apr 10, 2024
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  3. add comment line

    fmalmeida committed Apr 10, 2024
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  4. fix namings

    fmalmeida committed Apr 10, 2024
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  5. fix if-else and .join() operations

    fmalmeida committed Apr 10, 2024
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  6. fix selected data

    fmalmeida committed Apr 10, 2024
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  7. fix testing size

    fmalmeida committed Apr 10, 2024
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  8. change to workDir

    fmalmeida committed Apr 10, 2024
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  9. avoid always writing to allow caching

    fmalmeida committed Apr 10, 2024
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  10. starting conversion as module

    fmalmeida committed Apr 10, 2024
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Commits on Apr 11, 2024

  1. converted parsing and split to a module

    fmalmeida committed Apr 11, 2024
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  2. fix code for ensuring FIFO

    fmalmeida committed Apr 11, 2024
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  3. fixed cellranger-multi input channel logic

    fmalmeida committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. solved cellranger multi parsing and pipeline execution

    fmalmeida committed Apr 12, 2024
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Commits on Apr 15, 2024

  1. add first cellranger-multi try-out bugfixes

    fmalmeida committed Apr 15, 2024
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  2. Fix renaming logic

    @grst
    grst committed Apr 15, 2024
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Commits on Apr 16, 2024

  1. fix variable

    fmalmeida committed Apr 16, 2024
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Commits on Apr 17, 2024

  1. added frna probeset subset reference and include parsing in module

    fmalmeida committed Apr 17, 2024
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  2. frna runs also generate raw data per sample 

    let's standardize raw = unmultiplexed
    fmalmeida committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. use shared nf-core test-datasets

    fmalmeida committed Apr 18, 2024
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  2. update cellranger multi module

    fmalmeida committed Apr 18, 2024
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  3. add options-gex meta parsing

    fmalmeida committed Apr 18, 2024
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  4. Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 247-su… 

    …pport-for-10x-ffpe-scrna
    fmalmeida committed Apr 18, 2024
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  5. update last cellranger module

    fmalmeida committed Apr 18, 2024
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  6. adjust mkvdjref inputs

    fmalmeida committed Apr 18, 2024
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  7. fix double comma

    fmalmeida committed Apr 18, 2024
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  8. update 'channel checkings'

    fmalmeida committed Apr 18, 2024
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  9. add new parameter

    fmalmeida committed Apr 18, 2024
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  10. fix schema

    fmalmeida committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. also save config per sample

    fmalmeida committed Apr 19, 2024
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  2. add todo

    fmalmeida committed Apr 19, 2024
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  3. add fb reference example

    fmalmeida committed Apr 19, 2024
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Commits on Apr 22, 2024

  1. fix file saving and remove outdated workaround on mqc

    fmalmeida committed Apr 22, 2024
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  2. add an universal key in cellranger-multi data options map so that par… 

    …sing in module works fine to differentiate empty / real data
    fmalmeida committed Apr 22, 2024
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  3. update comment

    fmalmeida committed Apr 22, 2024
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  4. add new inputs to nf-test

    fmalmeida committed Apr 22, 2024
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  5. commit latest editions required in nf-core/module ( must be added in … 

    …central module )
    fmalmeida committed Apr 22, 2024
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Commits on Apr 29, 2024

  1. try test update

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. change global variable used

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed Apr 30, 2024
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  2. update test to use chr14

    @fmalmeida
    fmalmeida committed Apr 30, 2024
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  3. change reference and resources used

    @fmalmeida
    fmalmeida committed Apr 30, 2024
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  4. update number of tasks

    @fmalmeida
    fmalmeida committed Apr 30, 2024
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  5. Make it work without specifying GTF file

    @grst
    grst committed Apr 30, 2024
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  6. fix pre-commit

    @grst
    grst committed Apr 30, 2024
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Commits on May 1, 2024

  1. set working nf-test for cellranger multi

    @fmalmeida
    fmalmeida committed May 1, 2024
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  2. add .clone() method

    @fmalmeida
    fmalmeida committed May 1, 2024
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  3. decrease asked memory

    @fmalmeida
    fmalmeida committed May 1, 2024
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  4. make sure ArrayBag is cloned to avoid input modification

    @fmalmeida
    fmalmeida committed May 1, 2024
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  5. change name for a better explanation

    @fmalmeida
    fmalmeida committed May 1, 2024
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  6. modified by prettier

    @fmalmeida
    fmalmeida committed May 1, 2024
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  7. update resources in test profile

    @fmalmeida
    fmalmeida committed May 1, 2024
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  8. make sure the workflow can work with new version of module that does … 

    …not use 'EMPTY' file for references and rather uses []
    @fmalmeida
    fmalmeida committed May 1, 2024
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  9. fix mkgtf module "lint"

    @fmalmeida
    fmalmeida committed May 1, 2024
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  10. updated cellranger multi via nf-core tools

    @fmalmeida
    fmalmeida committed May 1, 2024
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  11. force deletion for lint

    @fmalmeida
    fmalmeida committed May 1, 2024
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  12. manually download correct images

    @fmalmeida
    fmalmeida committed May 1, 2024
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Commits on May 2, 2024

  1. Merge branch '247-support-for-10x-ffpe-scrna' into fix-without-gtf

    @fmalmeida
    fmalmeida committed May 2, 2024
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  2. Merge pull request #322 from nf-core/fix-without-gtf 

    Make it work without specifying GTF file
    @fmalmeida
    fmalmeida committed May 2, 2024
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Commits on May 6, 2024

  1. adjust parse to be the same for raw/filtered matrices

    @fmalmeida
    fmalmeida committed May 6, 2024
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  2. fix fastqc channel naming

    @fmalmeida
    fmalmeida committed May 6, 2024
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  3. update nf-tests

    @fmalmeida
    fmalmeida committed May 6, 2024
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  4. update name

    @fmalmeida
    fmalmeida committed May 6, 2024
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  5. use pre-made fastqc_multiqc channel

    @fmalmeida
    fmalmeida committed May 6, 2024
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  6. nf-core lint fix

    @fmalmeida
    fmalmeida committed May 6, 2024
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  7. flatten channel

    @fmalmeida
    fmalmeida committed May 6, 2024
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  8. update subworkflow

    @fmalmeida
    fmalmeida committed May 6, 2024
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Commits on May 7, 2024

  1. add missing .mix() operator

    @fmalmeida
    fmalmeida committed May 7, 2024
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Commits on May 10, 2024

  1. include cellrangermulti raw matrices for custom emptydrops filtering

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed May 10, 2024
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  2. correct indentation

    zxBIB Almeida,Felipe (GCBDS) EXTERNAL committed May 10, 2024
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  3. starting documentation on cellranger multi

    @fmalmeida
    fmalmeida committed May 10, 2024
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  4. continue documentation

    @fmalmeida
    fmalmeida committed May 10, 2024
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Commits on May 14, 2024

  1. update documentation

    @fmalmeida
    fmalmeida committed May 14, 2024
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  2. add section in outputs

    @fmalmeida
    fmalmeida committed May 14, 2024
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Commits on May 15, 2024

  1. Merge remote-tracking branch 'origin/dev' into 247-support-for-10x-ff… 

    …pe-scrna
    @grst
    grst committed May 15, 2024
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  2. Update usage

    @grst
    grst committed May 15, 2024
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  3. Fixed 'file-path' in nextflow schema

    @grst
    grst committed May 15, 2024
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  4. Update output documentation

    @grst
    grst committed May 15, 2024
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  5. Update nextflow_schema.json

    @grst
    grst committed May 15, 2024
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Commits on May 16, 2024

  1. remove gex_barcode_sample_assignment parameter

    @fmalmeida
    fmalmeida committed May 16, 2024
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  2. add note

    @fmalmeida
    fmalmeida committed May 16, 2024
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Commits on May 17, 2024

  1. Update nextflow schema documentation

    @grst
    grst committed May 17, 2024
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  2. Revert "remove gex_barcode_sample_assignment parameter" 

    This reverts commit 03a38cd.
    @grst
    grst committed May 17, 2024
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  3. Revert "add note" 

    This reverts commit e22f986.
    @grst
    grst committed May 17, 2024
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Commits on May 22, 2024

  1. Merge branch 'dev' into 247-support-for-10x-ffpe-scrna

    @maxulysse
    maxulysse committed May 22, 2024
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  2. update file

    @maxulysse
    maxulysse committed May 22, 2024
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  3. update file better

    @maxulysse
    maxulysse committed May 22, 2024
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