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Add umicollapse as an alternative to umi-tools #1369

Merged
merged 15 commits into from
Dec 4, 2024
Merged

Add umicollapse as an alternative to umi-tools #1369

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fc13650
Add umicollapse as an alternative to umi-tools
siddharthab Sep 3, 2024
761c56d
Keep umitools as the default
siddharthab Sep 4, 2024
acd8f65
Merge branch 'dev' into umicollapse
siddharthab Oct 29, 2024
e86e9a6
update umicollapse to 1.1.0
siddharthab Oct 29, 2024
28b10ac
update CHANGELOG
siddharthab Oct 29, 2024
e5d9d4b
actually update umicollapse
siddharthab Nov 5, 2024
05513ee
Apply suggestions from code review
siddharthab Nov 6, 2024
ee2dde2
Merge branch 'dev' into umicollapse
pinin4fjords Nov 12, 2024
b372821
[automated] Fix code linting
nf-core-bot Nov 12, 2024
88d6411
Update tests for UMICollapse module.
MatthiasZepper Nov 29, 2024
15116a3
Update umi-tools dedup tests at well.
MatthiasZepper Nov 29, 2024
3bbd907
Update tests in subworkflows as well.
MatthiasZepper Nov 29, 2024
79d52f6
Merge branch 'dev' into umicollapse
maxulysse Dec 4, 2024
450b5b9
Restore truncated CHANGELOG.md with 3.0 and prior releases.
MatthiasZepper Dec 4, 2024
a2dac87
[automated] Fix code linting
nf-core-bot Dec 4, 2024
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451 changes: 25 additions & 426 deletions CHANGELOG.md
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12 changes: 12 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -198,6 +198,7 @@
"branch": "master",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": [
"bam_dedup_stats_samtools_umicollapse",
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
"bam_sort_stats_samtools"
Expand Down Expand Up @@ -266,6 +267,11 @@
"git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"umicollapse": {
"branch": "master",
"git_sha": "78991a2306e7631c006498a372e87f135a4212db",
"installed_by": ["bam_dedup_stats_samtools_umicollapse"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
Expand All @@ -290,6 +296,11 @@
},
"subworkflows": {
"nf-core": {
"bam_dedup_stats_samtools_umicollapse": {
"branch": "master",
"git_sha": "78991a2306e7631c006498a372e87f135a4212db",
"installed_by": ["subworkflows"]
},
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
Expand All @@ -314,6 +325,7 @@
"branch": "master",
"git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
"installed_by": [
"bam_dedup_stats_samtools_umicollapse",
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
"bam_sort_stats_samtools"
Expand Down
5 changes: 5 additions & 0 deletions modules/nf-core/umicollapse/environment.yml
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73 changes: 73 additions & 0 deletions modules/nf-core/umicollapse/main.nf
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82 changes: 82 additions & 0 deletions modules/nf-core/umicollapse/meta.yml
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