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Blastn #81

Closed
wants to merge 69 commits into from
Closed

Blastn #81

wants to merge 69 commits into from

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alxndrdiaz
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Alexander Ramos-Diaz and others added 30 commits May 23, 2023 02:33
added chunk_busco module
b2e2e06
@alxndrdiaz
added diamond_blastx module
a833404
@alxndrdiaz
added blastx_cols and blastx_outext
94b44c9
@alxndrdiaz
fix DIAMOND_BLASTX path
46ae681
@alxndrdiaz
added module BLOBTOOLKIT_UNCHUNK
b5594c4
@alxndrdiaz
diamond_blastx data for test_full
4c3e944
@alxndrdiaz
removed log files
40c212a
@alxndrdiaz
fix path to uniprot_blastx
0ae6480
@alxndrdiaz
renamed files in RUN_BLASTX subworkflow
a7502f0
@alxndrdiaz
use meta and meta2
8de106a
@alxndrdiaz
use names in RUN_BLASTX input channels
5466144
@alxndrdiaz
added uniprot_blastx
d667473
merge blastx results in BlobDir
49cb8bf
@alxndrdiaz
minimum Nextflow version 23.04.1
abc2b97
@alxndrdiaz
update uniprot databases
7bd7873
@alxndrdiaz
updated paths to uniprot databases
cec0022
@alxndrdiaz @priyanka-surana
Update conf/test.config
ddb9645 
change uniprot database names

Co-authored-by: Priyanka Surana <[email protected]>
@alxndrdiaz
use new names for uniprot databases
d814e5f
@alxndrdiaz @priyanka-surana
Update modules/local/blobtoolkit/chunk.nf
3bc14aa 
Co-authored-by: Priyanka Surana <[email protected]>
@alxndrdiaz
update names for uniprot databases
72f040c
@alxndrdiaz
fix description
0dbc9b6
@alxndrdiaz
update uniprot database names
c8bef6c
@alxndrdiaz
check params.blastp and params.blastx
1c9f9c4
@alxndrdiaz
independent channels in RUN_BLASTX
8f3f719
@alxndrdiaz
added module NOHIT_LIST
0c61987
@alxndrdiaz
added subworkflow RUN_BLASTN
8c3936a
@alxndrdiaz
NOHIT_LIST parameters
5c6365a
@alxndrdiaz
include RUN_BLASTN subworkflow
0a988e4
@alxndrdiaz
use shell block
20a4784
@alxndrdiaz
update RUN_BLASTN input
d9411a0
@alxndrdiaz alxndrdiaz requested a review from muffato July 19, 2023 03:37
@alxndrdiaz alxndrdiaz self-assigned this Jul 19, 2023
@alxndrdiaz alxndrdiaz added the enhancement Improvement of the existing features label Jul 19, 2023
@alxndrdiaz alxndrdiaz linked an issue Jul 19, 2023 that may be closed by this pull request
subworkflow: blastn #21
Closed
@alxndrdiaz alxndrdiaz added this to the 0.2.0 milestone Jul 19, 2023
@alxndrdiaz

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@muffato muffato changed the base branch from main to dev September 5, 2023 07:24
@priyanka-surana
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Closing and opening a new one for a final merge. Give me a couple days.

@priyanka-surana priyanka-surana deleted the blastn branch December 16, 2023 17:15
@priyanka-surana priyanka-surana restored the blastn branch December 16, 2023 18:53
@priyanka-surana priyanka-surana deleted the blastn branch December 16, 2023 19:08
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Reviewers

@priyanka-surana priyanka-surana Awaiting requested review from priyanka-surana

@muffato muffato Awaiting requested review from muffato

Assignees

@alxndrdiaz alxndrdiaz

Labels
enhancement Improvement of the existing features
Projects
BlobToolKit Nextflow Pipeline
Status: Done
Milestone
0.2.0
Development

Successfully merging this pull request may close these issues.

subworkflow: blastn
3 participants
@alxndrdiaz @priyanka-surana @muffato