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.

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

Update bedtools, blast, minimap2, etc. container images #361

Merged
merged 5 commits into from
Nov 10, 2023
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
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
Original file line number Diff line number Diff line change
Expand Up @@ -47,8 +47,8 @@ class BedtoolsIntersectArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Bedtools executable. Defaults to bedtools.")
var executable: String = "bedtools"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.30.0--h468198e_3.")
var image: String = "quay.io/biocontainers/bedtools:2.30.0--h468198e_3"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_0.")
var image: String = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
Expand Down
4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala
Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,8 @@ class BlastnArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the blastn executable. Defaults to blastn.")
var executable: String = "blastn"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.13.0--hf3cf87c_0.")
var image: String = "quay.io/biocontainers/blast:2.13.0--hf3cf87c_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_0.")
var image: String = "quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
Expand Down
4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala
Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,8 @@ class Bowtie2Args extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie 2 executable. Defaults to bowtie2.")
var executable: String = "bowtie2"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.1--py310h8d7afc0_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.1--py310h8d7afc0_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
Expand Down
4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala
Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,8 @@ class Minimap2Args extends ReadGroupArgs {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Minimap2 executable. Defaults to minimap2.")
var executable: String = "minimap2"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.24--h7132678_1.")
var image: String = "quay.io/biocontainers/minimap2:2.24--h7132678_1"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.25--h7132678_0.")
var image: String = "quay.io/biocontainers/minimap2:2.25--h7132678_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,8 @@ class SingleEndBowtie2Args extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie 2 executable. Defaults to bowtie2.")
var executable: String = "bowtie2"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.0--py310h8d7afc0_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.0--py310h8d7afc0_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
Expand Down
Loading