feat: Support for 3-prime RNA sequencing #62

manuelphilip · 2022-10-07T11:28:24Z

No description provided.

Added heatmap and QC plot to report.html

…rna-seq-kallisto-sleuth into 3-prime-rna

…s and updated codes

…hway plot

…scripts for 3prime quantification

johanneskoester

Epic work, thanks a lot! I have various requests below.

workflow/Snakefile

workflow/envs/QC.yaml

workflow/envs/aligned_pos.yaml

workflow/envs/canonical_reads.yaml

workflow/scripts/get_histogram.py

workflow/scripts/get_pathway_barplot.R

workflow/scripts/get_pathway_barplot.py

workflow/scripts/plot_ind-transcripts_histogram.py

workflow/scripts/sleuth-diffexp.R

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

config/config.yaml

workflow/rules/common.smk

workflow/rules/trim_3prime.smk

workflow/rules/diffexp.smk

workflow/rules/qc_3prime.smk

workflow/rules/diffexp.smk

🤖 I have created a release *beep* *boop* --- ## [2.5.0](v2.4.3...v2.5.0) (2023-05-13) ### Features * Support for 3-prime RNA sequencing ([#62](#62)) ([c06c573](c06c573)) ### Bug Fixes * fix report labels ([#72](#72)) ([76c7fd9](76c7fd9)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

johanneskoester and others added 26 commits June 2, 2022 12:05

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

849ed48

add a rule for obtaining the maximum read length after trimming

f8702fd

remove unnecessary parameter

55a1fe6

add script

2bc7a0a

add env

381cfbc

test push

33dbb58

added 3prime reference seq fetch code

fa2e575

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

e560178

added script for histogram and 3prime from cds

5eaa67d

added heatmap script for top 50 var genes

d88dbdd

added histogram and heatmap scripts

391af4c

Modified the histogram plot and heatmap scripts

bfbcdfb

Updated histogram plot and dependency workflows

a1cce49

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

e651835

Added heatmap and QC plot to report.html

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

d990322

…rna-seq-kallisto-sleuth into 3-prime-rna

resovled merge issue happened

e5426c8

modifed script get_3prime-seq.py

2e5be41

updated workflow that includes filtering out non-canonical transcript…

5a179bf

…s and updated codes

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

5697b3c

…hway plot

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

26efc57

…scripts for 3prime quantification

updated cutadapt rule for 3prime reads and dependencies

42aa1ae

updated config file and dependencies

4412dd1

update code plot_ind-transcripts_histogram.py and its dependencies

81c90ff

renamed file plot_ind-transcripts_histogram.py

e34a894

Added plot-qc: all to config file

e486860

Merge branch 'main' into 3-prime-rna

664b48e

johanneskoester requested changes Oct 11, 2022

View reviewed changes

manuelphilip and others added 3 commits October 11, 2022 16:19

Update workflow/envs/QC.yaml

24e52ed

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

Update workflow/envs/aligned_pos.yaml

b2f6d4b

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

Update workflow/envs/canonical_reads.yaml

72daaa0

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

manuelphilip added 10 commits March 9, 2023 16:41

check space of .test

f54c1d3

check .testspace

6db5cdb

updated .test folder space

9ed3f07

check space in .test

68e60b4

updated main.yaml file

f5ac8f4

Updated args for number of cores due to lack of memory

5a5c475

Split into individual jobs in main.yaml

caf308b

Fix main.yaml

68bd3c3

Fix heatmap plot width in pdf

a4fc8a0

Fix heatmap width while plotting in pdf

bff05ce

johanneskoester requested changes Mar 13, 2023

View reviewed changes

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

e2471fd

johanneskoester requested changes Mar 17, 2023

View reviewed changes

workflow/rules/trim_3prime.smk Outdated Show resolved Hide resolved

updated snakemake report removed redundant files/labels defined.

0dd5406

johanneskoester requested changes Mar 29, 2023

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Manuel Philip added 2 commits March 29, 2023 16:27

updated label config

4871dd6

fix formatting

07f54cc

johanneskoester requested changes Mar 31, 2023

View reviewed changes

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Manuel Philip added 7 commits April 27, 2023 15:24

Updated Volcano plot/enrichment and spia datavzrd tables

fb9dc11

Fix formatting diffexp.smk

8639c25

fix spia output file

764af83

Updated datavzrd version and its dependencies

52f1dc2

Fix diffexp.smk formatting

a40a218

updated main.yamlfile

9a31873

Set pandas version in QC.yaml to 1

0c78cf6

johanneskoester approved these changes May 12, 2023

View reviewed changes

johanneskoester merged commit c06c573 into main May 12, 2023

johanneskoester deleted the 3-prime-rna branch May 12, 2023 12:27

github-actions bot mentioned this pull request May 12, 2023

chore(main): release 2.5.0 #71

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feat: Support for 3-prime RNA sequencing #62

feat: Support for 3-prime RNA sequencing #62

manuelphilip commented Oct 7, 2022

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feat: Support for 3-prime RNA sequencing #62

feat: Support for 3-prime RNA sequencing #62

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