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fix: Updated the get-transcript-info.R file and its dependencies #73

Merged
merged 156 commits into from
Jun 14, 2023
Merged

fix: Updated the get-transcript-info.R file and its dependencies #73

merged 156 commits into from
Jun 14, 2023

Commits on Jun 2, 2022

  1. feat: added skeleton for 3-prime RNA-seq analysis

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    johanneskoester committed Jun 2, 2022
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Commits on Jun 22, 2022

  1. add a rule for obtaining the maximum read length after trimming

    @johanneskoester
    johanneskoester committed Jun 22, 2022
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  2. remove unnecessary parameter

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    johanneskoester committed Jun 22, 2022
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  3. add script

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    johanneskoester committed Jun 22, 2022
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  4. add env

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    johanneskoester committed Jun 22, 2022
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Commits on Jun 23, 2022

  1. test push

    Manuel Philip committed Jun 23, 2022
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Commits on Jun 27, 2022

  1. added 3prime reference seq fetch code

    Manuel Philip committed Jun 27, 2022
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Commits on Jul 7, 2022

  1. updated the script get-3prime-seqs.R with 'coding' seqs

    Manuel Philip committed Jul 7, 2022
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Commits on Jul 26, 2022

  1. added script for histogram and 3prime from cds

    Manuel Philip committed Jul 26, 2022
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Commits on Aug 3, 2022

  1. added heatmap script for top 50 var genes

    Manuel Philip committed Aug 3, 2022
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Commits on Aug 5, 2022

  1. added histogram and heatmap scripts

    Manuel Philip committed Aug 5, 2022
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Commits on Aug 17, 2022

  1. Modified the histogram plot and heatmap scripts

    Manuel Philip committed Aug 17, 2022
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Commits on Aug 23, 2022

  1. Updated histogram plot and dependency workflows

    Manuel Philip committed Aug 23, 2022
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Commits on Aug 26, 2022

  1. modified workflow with is-3-prime-rna-seq: true/false 

    Added heatmap and QC plot to report.html
    @manuelphilip
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  2. Merge branch '3-prime-rna' of https://github.com/snakemake-workflows/… 

    …rna-seq-kallisto-sleuth into 3-prime-rna
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  3. resovled merge issue happened

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  4. modifed script get_3prime-seq.py

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Commits on Sep 1, 2022

  1. updated workflow that includes filtering out non-canonical transcript… 

    …s and updated codes
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Commits on Sep 2, 2022

  1. fixed unfiltering of canonical transcripts and added rst file for pat… 

    …hway plot
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Commits on Sep 28, 2022

  1. updated QC plot and workflow to get aligned reads from canonical tran… 

    …scripts for 3prime quantification
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Commits on Oct 4, 2022

  1. updated cutadapt rule for 3prime reads and dependencies

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Commits on Oct 5, 2022

  1. updated config file and dependencies

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Commits on Oct 6, 2022

  1. update code plot_ind-transcripts_histogram.py and its dependencies

    @manuelphilip
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  2. renamed file plot_ind-transcripts_histogram.py

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  3. Added plot-qc: all to config file

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Commits on Oct 11, 2022

  1. Merge branch 'main' into 3-prime-rna

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  2. Update workflow/envs/QC.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  3. Update workflow/envs/aligned_pos.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 11, 2022
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Commits on Oct 27, 2022

  1. Update workflow/envs/canonical_reads.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 27, 2022
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  2. Update workflow/envs/get_canonical_ids.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  3. Update config/config.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  4. Update config/config.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 27, 2022
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  5. Update workflow/envs/heatmap.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 27, 2022
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  6. Update workflow/envs/pysam.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  7. Update workflow/envs/r-fasta.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 27, 2022
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  8. Update workflow/report/plot-QC.rst 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 27, 2022
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  9. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 27, 2022
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  10. Update workflow/scripts/sleuth-diffexp.R 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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    manuelphilip and johanneskoester committed Oct 27, 2022
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Commits on Oct 28, 2022

  1. Added bwa rule and updated workflow and its dependencies.

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  2. Merge branch '3-prime-rna' of github.com:snakemake-workflows/rna-seq-… 

    …kallisto-sleuth into 3-prime-rna
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Commits on Nov 3, 2022

  1. Added spia-datavzd to report and updated workflow and its dependencies

    @manuelphilip
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  2. updated and renamed plot_ind-transcripts_histogram.py to `plot-ind-… 

    …sample-QC-histogram.py`
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Commits on Nov 16, 2022

  1. modified the workflow and auxiliary files for the QC plot

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Commits on Nov 24, 2022

  1. Updated kallisto rules and fix bugs in QC-plot script

    @manuelphilip
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Commits on Nov 30, 2022

  1. Add datavzrd tables for diffexp, go_terms and updated dependencies

    @manuelphilip
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Commits on Dec 1, 2022

  1. updated config.schema.yaml file and fix spia datavzrd bugs

    @manuelphilip
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  2. updated config.yaml

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  3. updated datavzrd version, diff exp tables

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Commits on Dec 2, 2022

  1. Merge branch 'main' into 3-prime-rna

    @johanneskoester
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  2. fixes

    @johanneskoester
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  3. fix

    @johanneskoester
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  4. fix formatting of cutadapt rules

    @johanneskoester
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  5. minor

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  6. fix config access for 3-prime-rna-seq keys

    @johanneskoester
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  7. added labels to datavzrd output

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  8. fix lints

    @johanneskoester
    johanneskoester committed Dec 2, 2022
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  9. fix quotes

    @johanneskoester
    johanneskoester committed Dec 2, 2022
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  10. fix quant for non-3-prime data

    @johanneskoester
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  11. fixes and categories

    @johanneskoester
    johanneskoester committed Dec 2, 2022
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  12. Fix folder path in kallisto_quant rule

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Commits on Dec 5, 2022

  1. updated datavzrd rule with volcano plot

    @manuelphilip
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  2. Merge branch '3-prime-rna' of github.com:snakemake-workflows/rna-seq-… 

    …kallisto-sleuth into 3-prime-rna
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Commits on Dec 9, 2022

  1. Fix kallisto input once 3-prime-rna-seq is set to false. Added volc… 

    …ano plots in datavzrd
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  2. fix formatting rule datavzrd

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  3. fix snakemake format for rule datavzrd

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Commits on Dec 15, 2022

  1. fix bugs when 3-prime-rna-seq set to false

    @manuelphilip
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  2. fix formatting

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  3. fix vega_plot_volcano.py bug

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Commits on Feb 1, 2023

  1. Create config.yaml

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  2. Update config.yaml

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  3. fixed formatting

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  4. updated cutadapt wrapper version

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  5. fix cutadapt se

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  6. added extra options to params in cutadapt rule

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  7. fix cutadapt se params

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  8. fixed cutadapt se bug

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  9. Update config.yaml

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  10. Added test case file for 3-prime-RNA data

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  11. Updated folder path of .test config and snakefile

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Commits on Feb 2, 2023

  1. updated .test raw fastq file path

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  2. Fix batch_effect to Batch_effect` in config.yaml

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  3. Fix bugs

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  4. updated main.yaml

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  5. Fix go significant terms sorting

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Commits on Feb 7, 2023

  1. Added 3prime specific smk files/updated dependencies

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  2. Merge branch 'main' into 3-prime-rna

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Commits on Feb 9, 2023

  1. updated workflow wrappers and dependencies

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  2. added pre-define-genelist in .test/3prime-config/config.yaml

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  3. added pre-define-genelist in .test/config.yaml

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  4. updated .test/3-prime-config/config.yaml

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  5. fix 3prime smk file bugs

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  6. Merge branch '3-prime-rna' of github.com:snakemake-workflows/rna-seq-… 

    …kallisto-sleuth into 3-prime-rna
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  7. updated go-enrichment-template.yaml file

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Commits on Feb 10, 2023

  1. Merge branch 'main' into 3-prime-rna

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Commits on Feb 13, 2023

  1. Updated differential expression heatmap script and dependencies

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  2. updated .test folder config.yaml file

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  3. Merge branch '3-prime-rna' of github.com:snakemake-workflows/rna-seq-… 

    …kallisto-sleuth into 3-prime-rna
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  4. fix formatting

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  5. Fix .test/config.yaml file

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  6. fix fgsea path in .test/3-prime-config/

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Commits on Feb 14, 2023

  1. fix fgsea path in .test/3-prime-config/

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  2. Update config/config.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  3. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  4. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  5. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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Commits on Feb 15, 2023

  1. Updated differential heatmap script and its dependencies

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  2. fix formatting common.smk

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Commits on Feb 17, 2023

  1. Update workflow/report/plot-heatmap.rst 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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  2. Update workflow/rules/diffexp.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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Commits on Feb 21, 2023

  1. updated differential expression rule and script

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Commits on Feb 22, 2023

  1. updated differential expression/spia script and dependencies

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Commits on Feb 23, 2023

  1. updated main.yaml for free space

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  2. fix main.yaml

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  3. updated main.yaml

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  4. added remove-android and remove-haskell to get more disk space

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  5. fix formatting main.yaml

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  6. fix formatting main.yaml

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  7. update main.yaml

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  8. update main.yaml

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  9. update main.yaml

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  10. update main.yaml

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  11. updated main.yaml

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  12. updated main.yaml file

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  13. updated main.yaml

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  14. updated main.yaml

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Commits on Mar 9, 2023

  1. update main.yaml file

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  2. fix main.yamlfile and snakefile

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  3. Fix path for 3-prime volcano_plot in test path

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  4. fix main.yaml file

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  5. check space of .test

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  6. check .testspace

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  7. updated .test folder space

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  8. check space in .test

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Commits on Mar 10, 2023

  1. updated main.yaml file

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  2. Updated args for number of cores due to lack of memory

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  3. Split into individual jobs in main.yaml

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  4. Fix main.yaml

    @manuelphilip
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  5. Fix heatmap plot width in pdf

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  6. Fix heatmap width while plotting in pdf

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Commits on Mar 14, 2023

  1. updated config.yaml/diffexp.smk and dependencies based on the comments

    Manuel Philip committed Mar 14, 2023
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Commits on Mar 22, 2023

  1. updated snakemake report removed redundant files/labels defined.

    Manuel Philip committed Mar 22, 2023
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Commits on Mar 29, 2023

  1. updated label config

    Manuel Philip committed Mar 29, 2023
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  2. fix formatting

    Manuel Philip committed Mar 29, 2023
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Commits on Apr 27, 2023

  1. Updated Volcano plot/enrichment and spia datavzrd tables

    Manuel Philip committed Apr 27, 2023
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  2. Fix formatting diffexp.smk

    Manuel Philip committed Apr 27, 2023
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Commits on Apr 28, 2023

  1. fix spia output file

    Manuel Philip committed Apr 28, 2023
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Commits on May 5, 2023

  1. Updated datavzrd version and its dependencies

    Manuel Philip committed May 5, 2023
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  2. Fix diffexp.smk formatting

    Manuel Philip committed May 5, 2023
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  3. updated main.yamlfile

    Manuel Philip committed May 5, 2023
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  4. Set pandas version in QC.yaml to 1

    Manuel Philip committed May 5, 2023
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Commits on Jun 1, 2023

  1. Fix transcript-info.Rscript for 3-prime-rna data and dependencies

    Manuel Philip committed Jun 1, 2023
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Commits on Jun 2, 2023

  1. Merge branch 'main' into 3-prime-rna

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  2. Fixed Conflicts

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Commits on Jun 6, 2023

  1. updated get-transcript-info.R for redundancy and code format

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Commits on Jun 13, 2023

  1. Added else case if mane_select not present in `get-transcript-info.… 

    …R code
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Commits on Jun 14, 2023

  1. Modified if else condition of mane_select in get-transcript-info.R

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