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Release 2.3 Updates: Fixes for contamination, UMI Handling, Template 2.11.1 #303

Merged
merged 126 commits into from
Jan 24, 2024
Merged

Release 2.3 Updates: Fixes for contamination, UMI Handling, Template 2.11.1 #303

merged 126 commits into from
Jan 24, 2024

Commits on May 10, 2022

  1. REVERT CHANGES 

    Reverting changes to a non-linted version and added the umitools modules.
    Christian Kubica authored and Christian Kubica committed May 10, 2022
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  2. INCLUDE UMITOOLS WORKFLOW 

    Added the umitools workflow and integrated it into the smrnaseq workflow
    Christian Kubica authored and Christian Kubica committed May 10, 2022
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Commits on May 13, 2022

  1. ADD DOCUMENTATION 

    Add additional documentation to use UMI tools as part of the pipeline.
Most of the documentation has been copied from nf-core/rnaseq.
    Christian Kubica authored and Christian Kubica committed May 13, 2022
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Commits on Jun 13, 2022

  1. ADD SAMTOOLS BAM2FQ MODULE 

    The bam2fq module is neccessary to convert the deduplicated bam
files back into a fastq format to be fed into the existing
pipeline.
    Christian Kubica authored and Christian Kubica committed Jun 13, 2022
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Commits on Jun 14, 2022

  1. ADD UMITOOLS EXTRACT ARGS 

    Added the umitools extract modules.config lines from nf-core/rnaseq
to this pipeline.
    Christian Kubica authored and Christian Kubica committed Jun 14, 2022
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Commits on Jun 15, 2022

  1. UPDATE MODULES.CONFIG 

    Added configurations for umi deduplication.
    Christian Kubica authored and Christian Kubica committed Jun 15, 2022
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  2. INCLUDE UMITOOLS DEDUP WORKFLOW 

    Initial comit of the umi dedup subworkflow. The workflow combines
already existing modules of the pipeline and nf-core module to
deduplicate the reads by mapping them to the species genome and
re-converting them to fastq after deduplication.
    Christian Kubica authored and Christian Kubica committed Jun 15, 2022
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  3. INCLUDE UMITOOLS DEDUP 

    includes the optional umitools deduplication step after the read
QC.
    Christian Kubica authored and Christian Kubica committed Jun 15, 2022
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  4. ADD SAMTOOLS SORT CONFIG 

    Added additional configuration to change the output file name of
samtools sort.
    @CKComputomics
    CKComputomics committed Jun 15, 2022
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  5. FIX TYPO

    @CKComputomics
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  6. ADD DEDUP DOCUMENTATION 

    Added the documentation detailing the output files of the UMI-tools
deduplication step.
    @CKComputomics
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  7. ADD DEDUP STEP

    @CKComputomics
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  8. ADD UMITOOLS VERSION

    @CKComputomics
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Commits on Jun 20, 2022

  1. MERGE DEDUPLICATED AND UNMAPPED READS AFTER DEDUPLICATION 

    After deduplication the reads that remained unaligned to the
provided reference genome are merged with the set of deduplicated
reads to enable the use of the full spectrum of reads, independent
of potential reference bias. This behaviour can be deactivated by
setting --umi_merge_unmapped false
    @CKComputomics
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  2. ADD MISSING OPTION

    @CKComputomics
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  3. ADD NEWLINE

    @CKComputomics
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Commits on Jun 21, 2022

  1. CLEAN CODE

    @CKComputomics
    CKComputomics committed Jun 21, 2022
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  2. ADD DOCUMENTATION

    @CKComputomics
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  3. ADD UMI_MERGE_UNMAPPED COMMAND

    @CKComputomics
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  4. FINALIZE DOCUMENTATION 

    Information on the new --umi_merge_unmapped command were added to
both the CHANGELOG, as well as the output markdown script.
    @CKComputomics
    CKComputomics committed Jun 21, 2022
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  5. UPDATE MAIL TEMPLATE

    @CKComputomics
    CKComputomics committed Jun 21, 2022
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  6. CHANGE DAG OUTPUT TO HTML

    @CKComputomics
    CKComputomics committed Jun 21, 2022
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  7. PLEASE PRETTIER

    @CKComputomics
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  8. Merge branch 'dev' into umitools

    @CKComputomics
    CKComputomics authored Jun 21, 2022
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  9. FIX MERGE ERROR

    @CKComputomics
    CKComputomics committed Jun 21, 2022
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  10. MAKE PRETTIER HAPPY

    @CKComputomics
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Commits on Jun 22, 2022

  1. ADD NF-CORE CAT 

    Includes the nf-core cat module to replace the custom concatenation
module.
    @CKComputomics
    CKComputomics committed Jun 22, 2022
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  2. REPLACE CUSTOM CAT WITH NF-CORE CAT 

    Implements the use of the nf-core cat module.
    @CKComputomics
    CKComputomics committed Jun 22, 2022
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  3. REMOVE UNUSED MODULE 

    deletes the now unused conatenation module.
    @CKComputomics
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Commits on Oct 12, 2023

  1. Re-organized code mirna_quant to make it simpler to read

    @sguizard
    sguizard committed Oct 12, 2023
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  2. Switched to HTML less hairpin.fa and mature.fa

    @sguizard
    sguizard committed Oct 12, 2023
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Commits on Oct 16, 2023

  1. detect bowtie2 idx instead of bowtie1 idx

    @sguizard
    sguizard committed Oct 16, 2023
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  2. print mirQuant inputs

    @sguizard
    sguizard committed Oct 16, 2023
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  3. debug mirdeeprun

    @sguizard
    sguizard committed Oct 16, 2023
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  4. remove previous debug print

    @sguizard
    sguizard committed Oct 16, 2023
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  5. add more debug messages

    @sguizard
    sguizard committed Oct 16, 2023
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  6. remove prints

    @sguizard
    sguizard committed Oct 16, 2023
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  7. remove metq from mature and hairpin

    @sguizard
    sguizard committed Oct 16, 2023
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  8. connect clean hairpin / mature to mirdeep2

    @sguizard
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  9. remove meta from fasta in mirdeep2_run

    @sguizard
    sguizard committed Oct 16, 2023
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  10. Clean debug prints

    @sguizard
    sguizard committed Oct 16, 2023
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  11. Merge branch 'debug' into fix-contamination_filter

    @sguizard
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Commits on Oct 17, 2023

  1. update bowtie map contaminant with right options

    @sguizard
    sguizard committed Oct 17, 2023
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  2. define args variable

    @sguizard
    sguizard committed Oct 17, 2023
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  3. FIx? - include fastqc trim to multiQC

    @sguizard
    sguizard committed Oct 17, 2023
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  4. Refresh pipeline summary

    @sguizard
    sguizard committed Oct 17, 2023
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  5. Fix version: missing quotes and misaligned END_VER

    @sguizard
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  6. Update doc with HTML less fa

    @sguizard
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Commits on Oct 18, 2023

  1. update mirtrace ouput directory

    @sguizard
    sguizard committed Oct 18, 2023
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  2. update fastqc config

    @sguizard
    sguizard committed Oct 18, 2023
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  3. Update mirdeep2 publish_dir path

    @sguizard
    sguizard committed Oct 18, 2023
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Commits on Nov 28, 2023

  1. Fix stats not executed from genome

    @fhausmann
    fhausmann committed Nov 28, 2023
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Commits on Dec 19, 2023

  1. Template update for nf-core/tools version 2.11

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Commits on Dec 20, 2023

  1. Template update for nf-core/tools version 2.11.1

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Commits on Jan 11, 2024

  1. Merge branch 'umi-handling' into umitools

    @apeltzer
    apeltzer authored Jan 11, 2024
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  2. Merge pull request #164 from CKComputomics/umitools 

    Merging this to the umihandling branch to be able to fix remaining bits there myself more easily. Please wait for the next PR to be opened, will post a link here.
    @apeltzer
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  3. First batch of updates to 2024

    @apeltzer
    apeltzer committed Jan 11, 2024
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  4. Add missing modules / subworkflows

    @apeltzer
    apeltzer committed Jan 11, 2024
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  5. Add issue to changelog

    @fhausmann
    fhausmann committed Jan 11, 2024
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  6. Bringing this to 2024

    @apeltzer
    apeltzer committed Jan 11, 2024
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  7. Merge branch 'umi-handling' into nf-core-template-merge-2.11.1

    @apeltzer
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  8. Fixing linting errors

    @apeltzer
    apeltzer committed Jan 11, 2024
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  9. Merge pull request #302 from nf-core/nf-core-template-merge-2.11.1 

    Important! Template update for nf-core/tools v2.11.1
    @apeltzer
    apeltzer authored Jan 11, 2024
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  10. Follow the lead, Timmy

    @apeltzer
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  11. Improvements to channel handling

    @apeltzer
    apeltzer committed Jan 11, 2024
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  12. Merge branch 'umi-handling' into fix_samtools_stats_genome

    @apeltzer
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  13. Merge pull request #300 from fhausmann/fix_samtools_stats_genome 

    Fix stats not executed from genome (fixes #299)
    @apeltzer
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Commits on Jan 12, 2024

  1. Update to latest subworkflow version

    @apeltzer
    apeltzer committed Jan 12, 2024
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  2. Cleaning up

    @apeltzer
    apeltzer committed Jan 12, 2024
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  3. Some more fixes / cleanup

    @apeltzer
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  4. Clean

    @apeltzer
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  5. Improved error handling

    @apeltzer
    apeltzer committed Jan 12, 2024
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  6. Update nextflow_schema.json

    @apeltzer
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  7. Merge remote-tracking branch 'upstream/fix-mirdeep2_and_contamination… 

    …_filter' into umi-handling
    @apeltzer
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  8. Fix for UMI fasta

    @apeltzer
    apeltzer committed Jan 12, 2024
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  9. Fix params.fasta

    @apeltzer
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  10. Minor updates

    @apeltzer
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  11. Fixing some lint warnings

    @apeltzer
    apeltzer committed Jan 12, 2024
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  12. Adding in versions for filter stats

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  13. Fixing more conda imports

    @apeltzer
    apeltzer committed Jan 12, 2024
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  14. More updates of modules

    @apeltzer
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  15. Fix

    @apeltzer
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  16. Fix

    @apeltzer
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  17. Another fix

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  18. Yeah fasta

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  19. Another one in the umi workflow

    @apeltzer
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  20. Update edger_qc

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Commits on Jan 17, 2024

  1. Shorten test.config

    @apeltzer
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  2. Adding in UMI tests

    @apeltzer
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  3. Addressing some reviews

    @apeltzer
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  4. Add UMI regex

    @apeltzer
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  5. Some more adjustments to make nf-core modules work

    @apeltzer
    apeltzer committed Jan 17, 2024
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  6. Fix meta2

    @apeltzer
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  7. Passing on meta2

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  8. use the channels, luke

    @apeltzer
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  9. Add better changelog with deps

    @apeltzer
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  10. Add updated modules

    @apeltzer
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  11. Add updated modules.json

    @apeltzer
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  12. Fixing the error :)

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Commits on Jan 18, 2024

  1. [automated] Fix linting with Prettier

    @nf-core-bot
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  2. This should fix umitools extract

    @apeltzer
    apeltzer committed Jan 18, 2024
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  3. Improve more modules

    @apeltzer
    apeltzer committed Jan 18, 2024
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  4. Less lines

    @apeltzer
    apeltzer committed Jan 18, 2024
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  5. Apply suggestions from code review 

    Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
    @apeltzer @maxulysse
    apeltzer and maxulysse authored Jan 18, 2024
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  6. Fix input cardinality

    @grst
    grst committed Jan 18, 2024
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  7. Compute index only once

    @grst
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  8. Check that fasta is provided when UMIs are used

    @grst
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  9. Acually use deduplicated reads

    @grst
    grst committed Jan 18, 2024
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  10. Use contaminant-filtered reads downstream

    @grst
    grst committed Jan 18, 2024
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  11. Ensure fasta is optional

    @grst
    grst committed Jan 18, 2024
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  12. Attempt to disable umi_stats on CI

    @grst
    grst committed Jan 18, 2024
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Commits on Jan 19, 2024

  1. increase limits for umitools dedup

    @grst
    grst committed Jan 19, 2024
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Commits on Jan 22, 2024

  1. Adding in possibiltiy to use different method for UMI grouping

    @apeltzer
    apeltzer committed Jan 22, 2024
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  2. Install umicollapse instead of umitools dedup

    @grst
    grst committed Jan 22, 2024
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  3. Switch to umicollapse

    @grst
    grst committed Jan 22, 2024
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  4. Switch to umicollapse

    @grst
    grst committed Jan 22, 2024
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  5. [automated] Fix linting with Prettier

    @nf-core-bot
    nf-core-bot committed Jan 22, 2024
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  6. Don't merge deduplicated fastqs with unmapped fastqs

    @grst
    grst committed Jan 22, 2024
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  7. Try to set heap size

    @grst
    grst committed Jan 22, 2024
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  8. cast heap size to int

    @grst
    grst committed Jan 22, 2024
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Commits on Jan 23, 2024

  1. Increase java stack size

    @grst
    grst committed Jan 23, 2024
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  2. Set jvm options via JAVA_TOOL_OPTIONS

    @grst
    grst committed Jan 23, 2024
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  3. Full manual mode

    @grst
    grst committed Jan 23, 2024
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  4. Use two-pass mode for umicollapse

    @grst
    grst committed Jan 23, 2024
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  5. Increase stack size even further

    @grst
    grst committed Jan 23, 2024
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Commits on Jan 24, 2024

  1. Updated umicollapse to modules provided version :)

    @apeltzer
    apeltzer committed Jan 24, 2024
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