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Fixing contamination_filter and mirdeep2 #294

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wants to merge 25 commits into from
Closed

Fixing contamination_filter and mirdeep2 #294

wants to merge 25 commits into from

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sguizard
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I tried to run the pipeline, but get some errors.
I studied the code and fix few things.

Here are the modifications I made:

  • Updated the doc to reflect the programs run by the pipeline (Trim Galore -> Fastp)
  • Replace the URLs of hairpin.fa and mature.fa to avoid having HTML code in the downloaded files
  • Fix MIRDEEP2 inputs channels
  • Fix bowtie_contaminant_map

I share my updates with you if you want to integrate them on nf-core repo.

@sguizard
Re-organized code mirna_quant to make it simpler to read
04b852c
@sguizard
Switched to HTML less hairpin.fa and mature.fa
f285867
@sguizard
detect bowtie2 idx instead of bowtie1 idx
6948bad
@sguizard
print mirQuant inputs
16bb675
@sguizard
debug mirdeeprun
90527a2
@sguizard
remove previous debug print
39f0597
@sguizard
add more debug messages
c198eda
@sguizard
remove prints
85cadb0
@sguizard
remove metq from mature and hairpin
7c703c9
@sguizard
connect clean hairpin / mature to mirdeep2
e8d04d2
@sguizard
remove meta from fasta in mirdeep2_run
9285dfb
@sguizard
Clean debug prints
3a3f11b
@sguizard
Merge branch 'debug' into fix-contamination_filter
357ca53
@sguizard
update bowtie map contaminant with right options
c6efa86
@sguizard
define args variable
0be5a17
@sguizard
FIx? - include fastqc trim to multiQC
13fc7a4
@sguizard
Refresh pipeline summary
71590db
@sguizard
Fix version: missing quotes and misaligned END_VER
892ab89
@sguizard
Update doc with HTML less fa
05ae65a
@sguizard
update mirtrace ouput directory
e6a0b75
@sguizard
update fastqc config
dd97948
@sguizard
Update mirdeep2 publish_dir path
b59a73f
@sguizard
Merge branch 'fix-mirdeep2_and_contamination_filter' into dev
ebf9b8e
@github-actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @sguizard,

It looks like this pull-request is has been made against the sguizard/smrnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the sguizard/smrnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@github-actions
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github-actions bot commented Oct 27, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2946ec7

+| ✅ 163 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSmrnaseq.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: save_merged

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-12 10:22:19

@sguizard sguizard changed the base branch from master to dev October 27, 2023 09:13
@lpantano
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Thanks! I was trying this URL: https://mirbase.org/download/hairpin.fa and it is failing for me right now. Do you know the stability of this link?

@lpantano
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oh, I guess mirbase is down right now.

@sguizard
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Thanks! I was trying this URL: https://mirbase.org/download/hairpin.fa and it is failing for me right now. Do you know the stability of this link?

I think the two links are pointing the exact same file.
The original one seems to have HTML UI to make the navigation/reading easier for the profane.
I am pretty confident about the stability.
I suppose the sed code that cleans the HTML from the fasta can be removed.

@apeltzer
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apeltzer commented Nov 2, 2023

Hm, that URL wasn't existing the last time we checked, thus the sed stuff got added to make sure we're cleaning up the files appropriately and then do not run into further trouble. I'm ok in dropping the sed code (as it simplifies things...) but am a bit hesitant as we had to change URLs a couple of times already 😓

@Daniel-Moreira-bio Daniel-Moreira-bio mentioned this pull request Dec 11, 2023
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@apeltzer apeltzer changed the base branch from dev to umi-handling January 12, 2024 10:14
@apeltzer
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Thanks @sguizard - I pulled in your changes & commits to #303

@apeltzer apeltzer closed this Jan 12, 2024
@apeltzer apeltzer mentioned this pull request Jan 24, 2024
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3 participants
@sguizard @lpantano @apeltzer