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Release/v1.0.0 #18

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ellendejong
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@ellendejong ellendejong commented Jan 21, 2025 •
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BasMonkey and others added 30 commits November 1, 2023 09:48
@BasMonkey
Fixed typo
ac7e437
@BasMonkey
Added star module
179a045
@BasMonkey
Added input channels for STAR Align
1933189
@BasMonkey
Refactor of gtf file path
e869c08
@rernst
Merge pull request #8 from UMCUGenetics/feature/star
db3d3c2 
Feature/star
added modules samtools, subread, umitools, and subworkflow bam_dedup_…
61fa628 
…stats_samtools_umitools
Merge branch 'feature/nf-core_clean' of https://github.com/UMCUGeneti…
028a068 
…cs/DxNextflowRNA into feature/nf-core_clean
@BasMonkey
Removed parent folder dots from include paths
d607f2e
@BasMonkey
Refactor of STAR_ALIGN output variables
4277b1b
@BasMonkey
Refactor of BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS input
ebd0c6d
@BasMonkey
Added ext.args for STAR_ALIGN process to handle fastq.gz
808dd9b
@rernst
Fix star for all fastq files
0383380
@BasMonkey
Added publish config for FASTQC, BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS an…
7da62e1 
…d SUBREAD_FEATURECOUNTS
@BasMonkey
Merge remote-tracking branch 'origin/feature/nf-core_clean' into feat…
e2177c3 
…ure/nf-core_clean
@rernst
Fix star for all fastq files
dc572e3
@rernst
Merge branch 'feature/nf-core_clean' of github.com:UMCUGenetics/DxNex…
0d96adb 
…tflowRNA into feature/nf-core_clean
@BasMonkey
Added Samtools sort module to pipeline
240d57d
@BasMonkey
Updated .gitignore with Jetbrains .idea folder
b066391
@rernst
Sort STAR output
ecfbdd3
@rernst
Merge branch 'feature/nf-core_clean' of github.com:UMCUGenetics/DxNex…
588a57d 
…tflowRNA into feature/nf-core_clean
@rernst
Remove space
3ea1e65
@BasMonkey
Replaced samtools sort with Samtools merge
b908417
@BasMonkey
Merge remote-tracking branch 'origin/feature/nf-core_clean' into feat…
15d019b 
…ure/nf-core_clean
@BasMonkey
Refactor of redundant SAMTOOLS sort function to merge
8c741cf
@rernst
Revert fromPath
a9dce9b
@rernst
Merge branch 'feature/nf-core_clean' of github.com:UMCUGenetics/DxNex…
fc8200b 
…tflowRNA into feature/nf-core_clean
@rernst
Block tools
60ee01d
@BasMonkey
Uncomments
ac96bc5
@BasMonkey
Added empty channels to SAMTOOLS_MERGE process
39fde5d
@rernst
Remove toList
751f126
ellendejong and others added 24 commits December 10, 2024 13:58
@ellendejong
Add report_comment and change order in multiqc_config.
0f05879
@ellendejong
update .nf-core.yml
641d6f0
@ellendejong
Add analysis_id outside workflow (in run.sh).
2c681a3
@ellendejong
Add CHANGELOG template.
307eeab
@ellendejong
Add code of conduct.
1245078
@ellendejong
Remove .docs from gitignore
c0e45ed
@ellendejong
Remove help from fasta
7f40fd4
@ellendejong
Update docs
854b7d7
@ellendejong
remove section nextflow_config.
fcbb8d4
@ellendejong
Auto-generate modules.json
13cd8ad
@ellendejong
Delete local copy of sortmerna and use modules.config to override con…
e053145 
…tainer to v4.3.7
@ellendejong
change location of sortmerna db fasta
fe6c43c
@ellendejong
Changed description to "UMCU Genetics RNA seq Workflow"
1a628b3
@ellendejong
Changed path to image
5326228
@ellendejong
Fix typo: L008
77287bf
@ellendejong
remove duplicate comment
20216af
@ellendejong
Delete local version of subworkflow utils_nfcore_pipeline
03ad7de
@ellendejong
Add sortmerna comments to explain sortmerna_reads vs sortmerna_index
3d23ec7
@ellendejong
Disable version detection to fix format FastQC version
2ad71f1
@ellendejong
Rename software versions column group.
5f9d0c3
@ellendejong
Harshil alignment formatting on local .nf files.
cd77fd2
@ellendejong
format documents
292da39
@ellendejong
Add export NONE
0a0c04d
@ellendejong
Merge pull request #17 from UMCUGenetics/feature/add_trimgalore
858e0ce 
fastq > cram using nf-core
@rernst rernst self-requested a review January 21, 2025 14:10
rernst
rernst previously approved these changes Jan 21, 2025
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Jorisvansteenbrugge
Jorisvansteenbrugge approved these changes Feb 3, 2025
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Changes look good and are consistent

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@Jorisvansteenbrugge Jorisvansteenbrugge Jorisvansteenbrugge approved these changes

@rernst rernst rernst left review comments

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@ellendejong @rernst @Jorisvansteenbrugge @BasMonkey @lonnekevanbrussel