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1.3.0 Release #109

Merged
merged 129 commits into from
Aug 22, 2024
Merged

1.3.0 Release #109

merged 129 commits into from
Aug 22, 2024

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tkchafin
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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).

muffato and others added 30 commits January 5, 2024 08:39
@muffato
Set use_work_dir_as_temp to true when running at the Sanger
5e76463
@muffato
Merge pull request #85 from sanger-tol/use_work_dir_as_temp
5231c09 
Set use_work_dir_as_temp to true when running at the Sanger
@muffato
Created a local module to convert to Fasta without intermediate files
e370b8c
@muffato
Simplified the topology of the pipeline by instantiating the CONVERT_…
04c160d 
…STATS sub-workflow just once
@muffato
Rolled out the minimap2 -I setting to all data types
6565f93
@muffato
Combined two consecutive samtools steps to save some space
b3cb5d8
@muffato
Sort the BAM file directly with bwamem2 to save some disk space
3d7a700
@muffato
Merged the markdup_stats sub-workflow into align_illumina
0e21eaf
@muffato
Updated the minimap2/align module to the latest nf-core version
3d71db7 
Now accepts a meta2 for the reference genome
@muffato
Updated the crumble module to keep it closer to the original
7a9671c
@muffato
We don't need the suspicious regions
cfb7977
@muffato
Also compress the Illumina files with crumble, and don't compress the…
20536ea 
… pre-cumble BAMs
@muffato
Not needed because crumble now outputs BAM
7cbb416
@muffato
Sort the BAM files before merging to make the output reproducible
c76d9a9
@muffato
Mistletoe (96Gbp, 2.4 M reads) takes 210 GB RAM and slightly over 2 h…
15ad23d 
…ours
@muffato
Merge tag '1.2.2' into dev
c3d0d44
@muffato
Memory settings for ALIGN_ONT:MINIMAP2_ALIGN
7ba557c
@muffato
Bumped the version and updated the changelog
92b4744
@muffato
The patch was missing
8299694
@muffato
Merge pull request #91 from sanger-tol/pipes
c5c53eb 
Pipes
@muffato
The patch is not needed anymore since I have combined this module wit…
bb7e6be 
…h SAMTOOLS_FASTQ into SAMTOOLS_FILTERTOFASTQ
@muffato
Merge pull request #94 from sanger-tol/samtools_view
f9be6aa 
Removed unneeded patch
@tkchafin
add --header optional argument
18cf836
@tkchafin
install nf-core/samtools/reheader module
7a11e6b
@tkchafin
install nf-core/samtools/reheader module
6fcc80a
@tkchafin
default config for samtools_reheader
55172c7
@tkchafin
switch to custom samtools reheader wrapper in local module
7a460b0
@tkchafin
switch to custom samtools reheader wrapper in local module
eeb3b29
@tkchafin
added subworkflow to insert custom sam header before cram generation
0e58ade
@tkchafin
example header template for profile/test
6e065b9
tkchafin and others added 22 commits August 12, 2024 09:56
@tkchafin
Merge pull request #102 from tkchafin/dev
eb95288 
merge bwamem_index and remove unneeded multiqc options
@tkchafin
nf-core modules install seqkit/fq2fa
8d32f1f
@tkchafin
nf-core modules install seqtk/subseq
33b0247
@tkchafin
added fastq option for pacbio input
dda1b1c
@tkchafin
prettier linting
e2a8d46
@tkchafin
added --outfmt and --compression arguments
458cfb5
@tkchafin
Merge pull request #106 from tkchafin/pacbio_fastq
02660d4 
Pacbio fastq
@tkchafin
Merge pull request #107 from tkchafin/output_options
1b91ed8 
Give user control of output format and compression
@tkchafin
Update CHANGELOG.md
e1492be
@tkchafin
Update README.md
5e4ad2a
@tkchafin
Update CHANGELOG.md
0560e28
@tkchafin
module updates for 1.3.0
1a0d590
@tkchafin
add new dependencies and parameters
198de2a
@tkchafin
Vernon 1.3.0
cd2c554
@tkchafin
Update CITATIONS.md
906d6dc
@tkchafin
ignore missing tower.yml
d2ed043
@tkchafin
remove unnedded tower.yml
a4ac213
@tkchafin
added new tool citations
9e6803d
@tkchafin
prettier linting
e189fe4
@tkchafin
new date
a141819
@muffato
Fixed a few occurrences of "nf-core"
a31b253
@tkchafin
Merge pull request #108 from tkchafin/1.3.0
1f1f240 
Version 1.3.0 pre-release
@tkchafin tkchafin changed the base branch from main to bam_output_tmp August 22, 2024 13:27
@tkchafin tkchafin changed the base branch from bam_output_tmp to bwamem_index August 22, 2024 13:37
@tkchafin tkchafin changed the base branch from bwamem_index to tmp_ci_ August 22, 2024 13:40
muffato
muffato approved these changes Aug 22, 2024
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@muffato muffato left a comment

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You'll change the base branch to main, right ?

@tkchafin tkchafin changed the base branch from tmp_ci_ to main August 22, 2024 20:30
@tkchafin tkchafin merged commit 52266c9 into main Aug 22, 2024
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3 participants
@tkchafin @muffato @reichan1998