Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add umicollapse as an alternative to umi-tools #1369

Open
wants to merge 12 commits into
base: dev
Choose a base branch
from
Open

Add umicollapse as an alternative to umi-tools #1369

Show file tree
Hide file tree
Changes from 6 commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
451 changes: 25 additions & 426 deletions CHANGELOG.md
View file
Open in desktop

Large diffs are not rendered by default.

12 changes: 12 additions & 0 deletions modules.json
View file
Open in desktop
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
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

73 changes: 73 additions & 0 deletions modules/nf-core/umicollapse/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

82 changes: 82 additions & 0 deletions modules/nf-core/umicollapse/meta.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading