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

Update Version of UMICollapse to 1.1.0 #6805

Merged
merged 4 commits into from
Nov 5, 2024
Merged

Update Version of UMICollapse to 1.1.0 #6805

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
a6e310e
Bump Version of UMICollapse to 1.1.0
MatthiasZepper Oct 18, 2024
92f4759
Update test snapshots for umicollapse.
MatthiasZepper Oct 22, 2024
b77720a
Merge branch 'master' into umicollapse_bump_1-1-0
MatthiasZepper Oct 29, 2024
5ac0db6
Merge branch 'master' into umicollapse_bump_1-1-0
sateeshperi Nov 5, 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
2 changes: 1 addition & 1 deletion modules/nf-core/umicollapse/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::umicollapse=1.0.0
- bioconda::umicollapse=1.1.0
6 changes: 3 additions & 3 deletions modules/nf-core/umicollapse/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ process UMICOLLAPSE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/umicollapse:1.0.0--hdfd78af_1' :
'biocontainers/umicollapse:1.0.0--hdfd78af_1' }"
'https://depot.galaxyproject.org/singularity/umicollapse:1.1.0--hdfd78af_0' :
'biocontainers/umicollapse:1.1.0--hdfd78af_0' }"

input:
tuple val(meta), path(input), path(bai)
Expand All @@ -24,7 +24,7 @@ process UMICOLLAPSE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.0.0-1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def VERSION = '1.1.0-0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
// Memory allocation: We need to make sure that both heap and stack size is sufficiently large for
// umicollapse. We set the stack size to 5% of the available memory, the heap size to 90%
// which leaves 5% for stuff happening outside of java without the scheduler killing the process.
Expand Down
3 changes: 2 additions & 1 deletion modules/nf-core/umicollapse/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ tools:
(UMIs)/Random Molecular Tags (RMTs)."
homepage: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse"
documentation: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse"
tool_dev_url: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse"
tool_dev_url: "https://github.com/siddharthab/UMICollapse"
MatthiasZepper marked this conversation as resolved.
Show resolved Hide resolved
doi: "10.7717/peerj.8275"
licence: ["MIT"]
identifier: ""
Expand Down Expand Up @@ -78,4 +78,5 @@ maintainers:
- "@CharlotteAnne"
- "@chris-cheshire"
- "@apeltzer"
- "@siddharthab"
- "@MatthiasZepper"
24 changes: 12 additions & 12 deletions modules/nf-core/umicollapse/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,14 @@
]
],
[
"versions.yml:md5,c1e0275d81b1c97a9344d216f9154996"
"versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-20T08:47:11.402203361"
"timestamp": "2024-10-22T10:43:04.890267074"
},
"umicollapse fastq tests": {
"content": [
Expand All @@ -32,14 +32,14 @@
]
],
[
"versions.yml:md5,c1e0275d81b1c97a9344d216f9154996"
"versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-01-30T10:45:56.053352008"
"timestamp": "2024-10-22T10:43:45.691571914"
},
"umicollapse stub tests": {
"content": [
Expand Down Expand Up @@ -112,13 +112,13 @@
]
],
[
"versions.yml:md5,c1e0275d81b1c97a9344d216f9154996"
"versions.yml:md5,03fdbcb1ba9bd40325ca42859d39deb1"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-20T08:47:30.028323337"
"timestamp": "2024-10-22T10:43:33.250587075"
}
}
4 changes: 2 additions & 2 deletions subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@
[
"versions.yml:md5,20605eb79c410c0ed179ba660d82f75b",
"versions.yml:md5,23617661d2c899996bee2b05db027e25",
"versions.yml:md5,268e43f34038d4c6146ed050630f95b4",
"versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7",
"versions.yml:md5,e02a62a393a833778e16542eeed0d148",
"versions.yml:md5,ef00762e264b99ac45713dc0dedf4060"
]
Expand All @@ -58,7 +58,7 @@
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-16T08:04:02.126366857"
"timestamp": "2024-10-22T10:44:38.266860983"
},
"test_bam_dedup_stats_samtools_umicollapse_idxstats": {
"content": [
Expand Down
Loading