Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat: Support for 3-prime RNA sequencing #62

Merged
merged 150 commits into from
May 12, 2023
Merged

feat: Support for 3-prime RNA sequencing #62

merged 150 commits into from
May 12, 2023

Commits on Jun 2, 2022

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

    @johanneskoester
    johanneskoester committed Jun 2, 2022
    Configuration menu
    Copy the full SHA
    849ed48 View commit details
    Browse the repository at this point in the history

Commits on Jun 22, 2022

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

    @johanneskoester
    johanneskoester committed Jun 22, 2022
    Configuration menu
    Copy the full SHA
    f8702fd View commit details
    Browse the repository at this point in the history

  2. remove unnecessary parameter

    @johanneskoester
    johanneskoester committed Jun 22, 2022
    Configuration menu
    Copy the full SHA
    55a1fe6 View commit details
    Browse the repository at this point in the history

  3. add script

    @johanneskoester
    johanneskoester committed Jun 22, 2022
    Configuration menu
    Copy the full SHA
    2bc7a0a View commit details
    Browse the repository at this point in the history

  4. add env

    @johanneskoester
    johanneskoester committed Jun 22, 2022
    Configuration menu
    Copy the full SHA
    381cfbc View commit details
    Browse the repository at this point in the history

Commits on Jun 23, 2022

  1. test push

    Manuel Philip committed Jun 23, 2022
    Configuration menu
    Copy the full SHA
    33dbb58 View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2022

  1. added 3prime reference seq fetch code

    Manuel Philip committed Jun 27, 2022
    Configuration menu
    Copy the full SHA
    fa2e575 View commit details
    Browse the repository at this point in the history

Commits on Jul 7, 2022

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

    Manuel Philip committed Jul 7, 2022
    Configuration menu
    Copy the full SHA
    e560178 View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2022

  1. added script for histogram and 3prime from cds

    Manuel Philip committed Jul 26, 2022
    Configuration menu
    Copy the full SHA
    5eaa67d View commit details
    Browse the repository at this point in the history

Commits on Aug 3, 2022

  1. added heatmap script for top 50 var genes

    Manuel Philip committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    d88dbdd View commit details
    Browse the repository at this point in the history

Commits on Aug 5, 2022

  1. added histogram and heatmap scripts

    Manuel Philip committed Aug 5, 2022
    Configuration menu
    Copy the full SHA
    391af4c View commit details
    Browse the repository at this point in the history

Commits on Aug 17, 2022

  1. Modified the histogram plot and heatmap scripts

    Manuel Philip committed Aug 17, 2022
    Configuration menu
    Copy the full SHA
    bfbcdfb View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2022

  1. Updated histogram plot and dependency workflows

    Manuel Philip committed Aug 23, 2022
    Configuration menu
    Copy the full SHA
    a1cce49 View commit details
    Browse the repository at this point in the history

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
    manuelphilip committed Aug 26, 2022
    Configuration menu
    Copy the full SHA
    e651835 View commit details
    Browse the repository at this point in the history

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

    …rna-seq-kallisto-sleuth into 3-prime-rna
    @manuelphilip
    manuelphilip committed Aug 26, 2022
    Configuration menu
    Copy the full SHA
    d990322 View commit details
    Browse the repository at this point in the history

  3. resovled merge issue happened

    @manuelphilip
    manuelphilip committed Aug 26, 2022
    Configuration menu
    Copy the full SHA
    e5426c8 View commit details
    Browse the repository at this point in the history

  4. modifed script get_3prime-seq.py

    @manuelphilip
    manuelphilip committed Aug 26, 2022
    Configuration menu
    Copy the full SHA
    2e5be41 View commit details
    Browse the repository at this point in the history

Commits on Sep 1, 2022

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

    …s and updated codes
    @manuelphilip
    manuelphilip committed Sep 1, 2022
    Configuration menu
    Copy the full SHA
    5a179bf View commit details
    Browse the repository at this point in the history

Commits on Sep 2, 2022

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

    …hway plot
    @manuelphilip
    manuelphilip committed Sep 2, 2022
    Configuration menu
    Copy the full SHA
    5697b3c View commit details
    Browse the repository at this point in the history

Commits on Sep 28, 2022

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

    …scripts for 3prime quantification
    @manuelphilip
    manuelphilip committed Sep 28, 2022
    Configuration menu
    Copy the full SHA
    26efc57 View commit details
    Browse the repository at this point in the history

Commits on Oct 4, 2022

  1. updated cutadapt rule for 3prime reads and dependencies

    @manuelphilip
    manuelphilip committed Oct 4, 2022
    Configuration menu
    Copy the full SHA
    42aa1ae View commit details
    Browse the repository at this point in the history

Commits on Oct 5, 2022

  1. updated config file and dependencies

    @manuelphilip
    manuelphilip committed Oct 5, 2022
    Configuration menu
    Copy the full SHA
    4412dd1 View commit details
    Browse the repository at this point in the history

Commits on Oct 6, 2022

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

    @manuelphilip
    manuelphilip committed Oct 6, 2022
    Configuration menu
    Copy the full SHA
    81c90ff View commit details
    Browse the repository at this point in the history

  2. renamed file plot_ind-transcripts_histogram.py

    @manuelphilip
    manuelphilip committed Oct 6, 2022
    Configuration menu
    Copy the full SHA
    e34a894 View commit details
    Browse the repository at this point in the history

  3. Added plot-qc: all to config file

    @manuelphilip
    manuelphilip committed Oct 6, 2022
    Configuration menu
    Copy the full SHA
    e486860 View commit details
    Browse the repository at this point in the history

Commits on Oct 11, 2022

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

    @johanneskoester
    johanneskoester authored Oct 11, 2022
    Configuration menu
    Copy the full SHA
    664b48e View commit details
    Browse the repository at this point in the history

  2. Update workflow/envs/QC.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 11, 2022
    Configuration menu
    Copy the full SHA
    24e52ed View commit details
    Browse the repository at this point in the history

  3. Update workflow/envs/aligned_pos.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 11, 2022
    Configuration menu
    Copy the full SHA
    b2f6d4b View commit details
    Browse the repository at this point in the history

Commits on Oct 27, 2022

  1. Update workflow/envs/canonical_reads.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    72daaa0 View commit details
    Browse the repository at this point in the history

  2. Update workflow/envs/get_canonical_ids.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    9139320 View commit details
    Browse the repository at this point in the history

  3. Update config/config.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    0d4faab View commit details
    Browse the repository at this point in the history

  4. Update config/config.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    eba5fb4 View commit details
    Browse the repository at this point in the history

  5. Update workflow/envs/heatmap.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    739cd14 View commit details
    Browse the repository at this point in the history

  6. Update workflow/envs/pysam.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    695236d View commit details
    Browse the repository at this point in the history

  7. Update workflow/envs/r-fasta.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    ca55ffe View commit details
    Browse the repository at this point in the history

  8. Update workflow/report/plot-QC.rst 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    16811e3 View commit details
    Browse the repository at this point in the history

  9. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    e1954d3 View commit details
    Browse the repository at this point in the history

  10. Update workflow/scripts/sleuth-diffexp.R 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Oct 27, 2022
    Configuration menu
    Copy the full SHA
    40c1ac9 View commit details
    Browse the repository at this point in the history

Commits on Oct 28, 2022

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

    @manuelphilip
    manuelphilip committed Oct 28, 2022
    Configuration menu
    Copy the full SHA
    f31cb99 View commit details
    Browse the repository at this point in the history

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

    …kallisto-sleuth into 3-prime-rna
    @manuelphilip
    manuelphilip committed Oct 28, 2022
    Configuration menu
    Copy the full SHA
    a57424a View commit details
    Browse the repository at this point in the history

Commits on Nov 3, 2022

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

    @manuelphilip
    manuelphilip committed Nov 3, 2022
    Configuration menu
    Copy the full SHA
    c204a20 View commit details
    Browse the repository at this point in the history

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

    …sample-QC-histogram.py`
    @manuelphilip
    manuelphilip committed Nov 3, 2022
    Configuration menu
    Copy the full SHA
    cdd0fc6 View commit details
    Browse the repository at this point in the history

Commits on Nov 16, 2022

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

    @manuelphilip
    manuelphilip committed Nov 16, 2022
    Configuration menu
    Copy the full SHA
    aa90b63 View commit details
    Browse the repository at this point in the history

Commits on Nov 24, 2022

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

    @manuelphilip
    manuelphilip committed Nov 24, 2022
    Configuration menu
    Copy the full SHA
    835d05c View commit details
    Browse the repository at this point in the history

Commits on Nov 30, 2022

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

    @manuelphilip
    manuelphilip committed Nov 30, 2022
    Configuration menu
    Copy the full SHA
    1c1081a View commit details
    Browse the repository at this point in the history

Commits on Dec 1, 2022

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

    @manuelphilip
    manuelphilip committed Dec 1, 2022
    Configuration menu
    Copy the full SHA
    7aa5a84 View commit details
    Browse the repository at this point in the history

  2. updated config.yaml

    @manuelphilip
    manuelphilip committed Dec 1, 2022
    Configuration menu
    Copy the full SHA
    2680e4d View commit details
    Browse the repository at this point in the history

  3. updated datavzrd version, diff exp tables

    @manuelphilip
    manuelphilip committed Dec 1, 2022
    Configuration menu
    Copy the full SHA
    f7ef4dd View commit details
    Browse the repository at this point in the history

Commits on Dec 2, 2022

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

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    5e99ab5 View commit details
    Browse the repository at this point in the history

  2. fixes

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    6add9aa View commit details
    Browse the repository at this point in the history

  3. fix

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    10d960f View commit details
    Browse the repository at this point in the history

  4. fix formatting of cutadapt rules

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    890620f View commit details
    Browse the repository at this point in the history

  5. minor

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    b5be7d7 View commit details
    Browse the repository at this point in the history

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

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    1dcdac4 View commit details
    Browse the repository at this point in the history

  7. added labels to datavzrd output

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    bdb9ec7 View commit details
    Browse the repository at this point in the history

  8. fix lints

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    f2796ce View commit details
    Browse the repository at this point in the history

  9. fix quotes

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    17c531c View commit details
    Browse the repository at this point in the history

  10. fix quant for non-3-prime data

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    0dbdd83 View commit details
    Browse the repository at this point in the history

  11. fixes and categories

    @johanneskoester
    johanneskoester committed Dec 2, 2022
    Configuration menu
    Copy the full SHA
    50574b7 View commit details
    Browse the repository at this point in the history

  12. Fix folder path in kallisto_quant rule

    @manuelphilip
    manuelphilip authored Dec 2, 2022
    Configuration menu
    Copy the full SHA
    f0577eb View commit details
    Browse the repository at this point in the history

Commits on Dec 5, 2022

  1. updated datavzrd rule with volcano plot

    @manuelphilip
    manuelphilip committed Dec 5, 2022
    Configuration menu
    Copy the full SHA
    2ada6a2 View commit details
    Browse the repository at this point in the history

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

    …kallisto-sleuth into 3-prime-rna
    @manuelphilip
    manuelphilip committed Dec 5, 2022
    Configuration menu
    Copy the full SHA
    a4a4a95 View commit details
    Browse the repository at this point in the history

Commits on Dec 9, 2022

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

    …ano plots in datavzrd
    @manuelphilip
    manuelphilip committed Dec 9, 2022
    Configuration menu
    Copy the full SHA
    141a7d6 View commit details
    Browse the repository at this point in the history

  2. fix formatting rule datavzrd

    @manuelphilip
    manuelphilip committed Dec 9, 2022
    Configuration menu
    Copy the full SHA
    c448806 View commit details
    Browse the repository at this point in the history

  3. fix snakemake format for rule datavzrd

    @manuelphilip
    manuelphilip committed Dec 9, 2022
    Configuration menu
    Copy the full SHA
    9f95844 View commit details
    Browse the repository at this point in the history

Commits on Dec 15, 2022

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

    @manuelphilip
    manuelphilip committed Dec 15, 2022
    Configuration menu
    Copy the full SHA
    80d7a97 View commit details
    Browse the repository at this point in the history

  2. fix formatting

    @manuelphilip
    manuelphilip committed Dec 15, 2022
    Configuration menu
    Copy the full SHA
    bee1b6c View commit details
    Browse the repository at this point in the history

  3. fix vega_plot_volcano.py bug

    @manuelphilip
    manuelphilip committed Dec 15, 2022
    Configuration menu
    Copy the full SHA
    f50673c View commit details
    Browse the repository at this point in the history

Commits on Feb 1, 2023

  1. Create config.yaml

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    748ac56 View commit details
    Browse the repository at this point in the history

  2. Update config.yaml

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    79bc8d7 View commit details
    Browse the repository at this point in the history

  3. fixed formatting

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    8eee57f View commit details
    Browse the repository at this point in the history

  4. updated cutadapt wrapper version

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    d21b87e View commit details
    Browse the repository at this point in the history

  5. fix cutadapt se

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    6dc9af5 View commit details
    Browse the repository at this point in the history

  6. added extra options to params in cutadapt rule

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    d7c364b View commit details
    Browse the repository at this point in the history

  7. fix cutadapt se params

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    789f296 View commit details
    Browse the repository at this point in the history

  8. fixed cutadapt se bug

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    99a18bd View commit details
    Browse the repository at this point in the history

  9. Update config.yaml

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    4e7d22f View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    19c4793 View commit details
    Browse the repository at this point in the history

  11. Updated folder path of .test config and snakefile

    @manuelphilip
    manuelphilip authored Feb 1, 2023
    Configuration menu
    Copy the full SHA
    78c476b View commit details
    Browse the repository at this point in the history

Commits on Feb 2, 2023

  1. updated .test raw fastq file path

    @manuelphilip
    manuelphilip authored Feb 2, 2023
    Configuration menu
    Copy the full SHA
    4e1a913 View commit details
    Browse the repository at this point in the history

  2. Fix batch_effect to Batch_effect` in config.yaml

    @manuelphilip
    manuelphilip authored Feb 2, 2023
    Configuration menu
    Copy the full SHA
    5c5346e View commit details
    Browse the repository at this point in the history

  3. Fix bugs

    @manuelphilip
    manuelphilip authored Feb 2, 2023
    Configuration menu
    Copy the full SHA
    7287bf3 View commit details
    Browse the repository at this point in the history

  4. updated main.yaml

    @manuelphilip
    manuelphilip authored Feb 2, 2023
    Configuration menu
    Copy the full SHA
    38caa9c View commit details
    Browse the repository at this point in the history

  5. Fix go significant terms sorting

    @manuelphilip
    manuelphilip authored Feb 2, 2023
    Configuration menu
    Copy the full SHA
    edc8ddd View commit details
    Browse the repository at this point in the history

Commits on Feb 7, 2023

  1. Added 3prime specific smk files/updated dependencies

    @manuelphilip
    manuelphilip committed Feb 7, 2023
    Configuration menu
    Copy the full SHA
    c92afc3 View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Feb 7, 2023
    Configuration menu
    Copy the full SHA
    0f67ecb View commit details
    Browse the repository at this point in the history

Commits on Feb 9, 2023

  1. updated workflow wrappers and dependencies

    @manuelphilip
    manuelphilip committed Feb 9, 2023
    Configuration menu
    Copy the full SHA
    6fac807 View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Feb 9, 2023
    Configuration menu
    Copy the full SHA
    3bd7b92 View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Feb 9, 2023
    Configuration menu
    Copy the full SHA
    b7fd3e7 View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Feb 9, 2023
    Configuration menu
    Copy the full SHA
    e37fed3 View commit details
    Browse the repository at this point in the history

  5. fix 3prime smk file bugs

    @manuelphilip
    manuelphilip committed Feb 9, 2023
    Configuration menu
    Copy the full SHA
    fab67c4 View commit details
    Browse the repository at this point in the history

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

    …kallisto-sleuth into 3-prime-rna
    @manuelphilip
    manuelphilip committed Feb 9, 2023
    Configuration menu
    Copy the full SHA
    24432fd View commit details
    Browse the repository at this point in the history

  7. updated go-enrichment-template.yaml file

    @manuelphilip
    manuelphilip committed Feb 9, 2023
    Configuration menu
    Copy the full SHA
    3721489 View commit details
    Browse the repository at this point in the history

Commits on Feb 10, 2023

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

    @manuelphilip
    manuelphilip authored Feb 10, 2023
    Configuration menu
    Copy the full SHA
    a555328 View commit details
    Browse the repository at this point in the history

Commits on Feb 13, 2023

  1. Updated differential expression heatmap script and dependencies

    @manuelphilip
    manuelphilip committed Feb 13, 2023
    Configuration menu
    Copy the full SHA
    d6023b9 View commit details
    Browse the repository at this point in the history

  2. updated .test folder config.yaml file

    @manuelphilip
    manuelphilip committed Feb 13, 2023
    Configuration menu
    Copy the full SHA
    b8bf9d1 View commit details
    Browse the repository at this point in the history

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

    …kallisto-sleuth into 3-prime-rna
    @manuelphilip
    manuelphilip committed Feb 13, 2023
    Configuration menu
    Copy the full SHA
    e8dee5e View commit details
    Browse the repository at this point in the history

  4. fix formatting

    @manuelphilip
    manuelphilip committed Feb 13, 2023
    Configuration menu
    Copy the full SHA
    f7d6438 View commit details
    Browse the repository at this point in the history

  5. Fix .test/config.yaml file

    @manuelphilip
    manuelphilip committed Feb 13, 2023
    Configuration menu
    Copy the full SHA
    ecafb97 View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Feb 13, 2023
    Configuration menu
    Copy the full SHA
    c7997b8 View commit details
    Browse the repository at this point in the history

Commits on Feb 14, 2023

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

    @manuelphilip
    manuelphilip authored Feb 14, 2023
    Configuration menu
    Copy the full SHA
    dfd6b25 View commit details
    Browse the repository at this point in the history

  2. Update config/config.yaml 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Feb 14, 2023
    Configuration menu
    Copy the full SHA
    78ea54b View commit details
    Browse the repository at this point in the history

  3. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Feb 14, 2023
    Configuration menu
    Copy the full SHA
    119b2e1 View commit details
    Browse the repository at this point in the history

  4. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Feb 14, 2023
    Configuration menu
    Copy the full SHA
    b753f89 View commit details
    Browse the repository at this point in the history

  5. Update workflow/rules/common.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Feb 14, 2023
    Configuration menu
    Copy the full SHA
    1dec9bb View commit details
    Browse the repository at this point in the history

Commits on Feb 15, 2023

  1. Updated differential heatmap script and its dependencies

    @manuelphilip
    manuelphilip committed Feb 15, 2023
    Configuration menu
    Copy the full SHA
    39e32f0 View commit details
    Browse the repository at this point in the history

  2. fix formatting common.smk

    @manuelphilip
    manuelphilip committed Feb 15, 2023
    Configuration menu
    Copy the full SHA
    33b571f View commit details
    Browse the repository at this point in the history

Commits on Feb 17, 2023

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

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Feb 17, 2023
    Configuration menu
    Copy the full SHA
    5a3a3f7 View commit details
    Browse the repository at this point in the history

  2. Update workflow/rules/diffexp.smk 

    Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
    @manuelphilip @johanneskoester
    manuelphilip and johanneskoester authored Feb 17, 2023
    Configuration menu
    Copy the full SHA
    d48ad74 View commit details
    Browse the repository at this point in the history

Commits on Feb 21, 2023

  1. updated differential expression rule and script

    @manuelphilip
    manuelphilip committed Feb 21, 2023
    Configuration menu
    Copy the full SHA
    0d60d7c View commit details
    Browse the repository at this point in the history

Commits on Feb 22, 2023

  1. updated differential expression/spia script and dependencies

    @manuelphilip
    manuelphilip committed Feb 22, 2023
    Configuration menu
    Copy the full SHA
    887fcff View commit details
    Browse the repository at this point in the history

Commits on Feb 23, 2023

  1. updated main.yaml for free space

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    16f4439 View commit details
    Browse the repository at this point in the history

  2. fix main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    c41fc28 View commit details
    Browse the repository at this point in the history

  3. updated main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    0b905dd View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    41573ff View commit details
    Browse the repository at this point in the history

  5. fix formatting main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    0c3e033 View commit details
    Browse the repository at this point in the history

  6. fix formatting main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    23d521d View commit details
    Browse the repository at this point in the history

  7. update main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    ea92da8 View commit details
    Browse the repository at this point in the history

  8. update main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    3b4cf95 View commit details
    Browse the repository at this point in the history

  9. update main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    b7508fb View commit details
    Browse the repository at this point in the history

  10. update main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    67dea25 View commit details
    Browse the repository at this point in the history

  11. updated main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    f47d6b2 View commit details
    Browse the repository at this point in the history

  12. updated main.yaml file

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    f6b10b8 View commit details
    Browse the repository at this point in the history

  13. updated main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    2cee69f View commit details
    Browse the repository at this point in the history

  14. updated main.yaml

    @manuelphilip
    manuelphilip authored Feb 23, 2023
    Configuration menu
    Copy the full SHA
    ce72da3 View commit details
    Browse the repository at this point in the history

Commits on Mar 9, 2023

  1. update main.yaml file

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    e0a565f View commit details
    Browse the repository at this point in the history

  2. fix main.yamlfile and snakefile

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    e6a6598 View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    2b61454 View commit details
    Browse the repository at this point in the history

  4. fix main.yaml file

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    f4cafd6 View commit details
    Browse the repository at this point in the history

  5. check space of .test

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    f54c1d3 View commit details
    Browse the repository at this point in the history

  6. check .testspace

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    6db5cdb View commit details
    Browse the repository at this point in the history

  7. updated .test folder space

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    9ed3f07 View commit details
    Browse the repository at this point in the history

  8. check space in .test

    @manuelphilip
    manuelphilip authored Mar 9, 2023
    Configuration menu
    Copy the full SHA
    68e60b4 View commit details
    Browse the repository at this point in the history

Commits on Mar 10, 2023

  1. updated main.yaml file

    @manuelphilip
    manuelphilip authored Mar 10, 2023
    Configuration menu
    Copy the full SHA
    f5ac8f4 View commit details
    Browse the repository at this point in the history

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

    @manuelphilip
    manuelphilip authored Mar 10, 2023
    Configuration menu
    Copy the full SHA
    5a5c475 View commit details
    Browse the repository at this point in the history

  3. Split into individual jobs in main.yaml

    @manuelphilip
    manuelphilip authored Mar 10, 2023
    Configuration menu
    Copy the full SHA
    caf308b View commit details
    Browse the repository at this point in the history

  4. Fix main.yaml

    @manuelphilip
    manuelphilip authored Mar 10, 2023
    Configuration menu
    Copy the full SHA
    68bd3c3 View commit details
    Browse the repository at this point in the history

  5. Fix heatmap plot width in pdf

    @manuelphilip
    manuelphilip committed Mar 10, 2023
    Configuration menu
    Copy the full SHA
    a4fc8a0 View commit details
    Browse the repository at this point in the history

  6. Fix heatmap width while plotting in pdf

    @manuelphilip
    manuelphilip committed Mar 10, 2023
    Configuration menu
    Copy the full SHA
    bff05ce View commit details
    Browse the repository at this point in the history

Commits on Mar 14, 2023

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

    Manuel Philip committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    e2471fd View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2023

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

    Manuel Philip committed Mar 22, 2023
    Configuration menu
    Copy the full SHA
    0dd5406 View commit details
    Browse the repository at this point in the history

Commits on Mar 29, 2023

  1. updated label config

    Manuel Philip committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    4871dd6 View commit details
    Browse the repository at this point in the history

  2. fix formatting

    Manuel Philip committed Mar 29, 2023
    Configuration menu
    Copy the full SHA
    07f54cc View commit details
    Browse the repository at this point in the history

Commits on Apr 27, 2023

  1. Updated Volcano plot/enrichment and spia datavzrd tables

    Manuel Philip committed Apr 27, 2023
    Configuration menu
    Copy the full SHA
    fb9dc11 View commit details
    Browse the repository at this point in the history

  2. Fix formatting diffexp.smk

    Manuel Philip committed Apr 27, 2023
    Configuration menu
    Copy the full SHA
    8639c25 View commit details
    Browse the repository at this point in the history

Commits on Apr 28, 2023

  1. fix spia output file

    Manuel Philip committed Apr 28, 2023
    Configuration menu
    Copy the full SHA
    764af83 View commit details
    Browse the repository at this point in the history

Commits on May 5, 2023

  1. Updated datavzrd version and its dependencies

    Manuel Philip committed May 5, 2023
    Configuration menu
    Copy the full SHA
    52f1dc2 View commit details
    Browse the repository at this point in the history

  2. Fix diffexp.smk formatting

    Manuel Philip committed May 5, 2023
    Configuration menu
    Copy the full SHA
    a40a218 View commit details
    Browse the repository at this point in the history

  3. updated main.yamlfile

    Manuel Philip committed May 5, 2023
    Configuration menu
    Copy the full SHA
    9a31873 View commit details
    Browse the repository at this point in the history

  4. Set pandas version in QC.yaml to 1

    Manuel Philip committed May 5, 2023
    Configuration menu
    Copy the full SHA
    0c78cf6 View commit details
    Browse the repository at this point in the history