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Update container images for bcftools, bedtools, blast, bowtie, etc. #369

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Nov 9, 2024
Merged

Update container images for bcftools, bedtools, blast, bowtie, etc. #369

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5c0457a
Update freebayes container image to 1.3.8--h6a68c12_2.
heuermh Nov 9, 2024
1669fcd
Update container images for bcftools, bedtools, blast, bowtie, bowtie…
heuermh Nov 9, 2024
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala
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Expand Up @@ -35,8 +35,8 @@ class BcftoolsCallArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the bcftools executable. Defaults to bcftools.")
var executable: String = "bcftools"

@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.20--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.21--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.21--h8b25389_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala
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Expand Up @@ -36,8 +36,8 @@ class BcftoolsMpileupArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the bcftools executable. Defaults to bcftools.")
var executable: String = "bcftools"

@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.20--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.21--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.21--h8b25389_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala
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Expand Up @@ -39,8 +39,8 @@ class BcftoolsNormArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the bcftools executable. Defaults to bcftools.")
var executable: String = "bcftools"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.20--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.20--h8b25389_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bcftools:1.21--h8b25389_0.")
var image: String = "quay.io/biocontainers/bcftools:1.21--h8b25389_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala
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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:2.31.1--hf5e1c6e_0.")
var image: String = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2.")
var image: String = "quay.io/biocontainers/bedtools:2.31.1--hf5e1c6e_2"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala
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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:2.15.0--pl5321h6f7f691_0.")
var image: String = "quay.io/biocontainers/blast:2.15.0--pl5321h6f7f691_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/blast:2.16.0--hc155240_2")
var image: String = "quay.io/biocontainers/blast:2.16.0--hc155240_2"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala
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Expand Up @@ -35,8 +35,8 @@ class BowtieArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Bowtie executable. Defaults to bowtie.")
var executable: String = "bowtie"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.3.1--py310h4070885_4.")
var image: String = "quay.io/biocontainers/bowtie:1.3.1--py310h4070885_4"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie:1.3.1--py311h73fc1d6_9.")
var image: String = "quay.io/biocontainers/bowtie:1.3.1--py311h73fc1d6_9"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala
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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/bowtie2:2.5.2--py39h6fed5c7_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.4--h7071971_4.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.4--h7071971_4"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala
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Expand Up @@ -38,8 +38,8 @@ class BwaMemArgs extends ReadGroupArgs {
@Args4jOption(required = false, name = "-executable", usage = "Path to the BWA executable. Defaults to bwa.")
var executable: String = "bwa"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa:0.7.18--he4a0461_0.")
var image: String = "quay.io/biocontainers/bwa:0.7.18--he4a0461_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa:0.7.18--he4a0461_1.")
var image: String = "quay.io/biocontainers/bwa:0.7.18--he4a0461_1"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala
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Expand Up @@ -38,8 +38,8 @@ class BwaMem2Args extends ReadGroupArgs {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Bwa-mem2 executable. Defaults to bwa-mem2.")
var executable: String = "bwa-mem2"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_2.")
var image: String = "quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_2"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_5.")
var image: String = "quay.io/biocontainers/bwa-mem2:2.2.1--hd03093a_5"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala
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Expand Up @@ -36,8 +36,8 @@ class FreebayesArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Freebayes executable. Defaults to freebayes.")
var executable: String = "freebayes"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/freebayes:1.3.6--hbfe0e7f_2.")
var image: String = "quay.io/biocontainers/freebayes:1.3.6--hbfe0e7f_2"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/freebayes:1.3.8--h6a68c12_2.")
var image: String = "quay.io/biocontainers/freebayes:1.3.8--h6a68c12_2"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala
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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/minimap2:2.27--he4a0461_1.")
var image: String = "quay.io/biocontainers/minimap2:2.27--he4a0461_1"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/minimap2:2.28--he4a0461_3.")
var image: String = "quay.io/biocontainers/minimap2:2.28--he4a0461_3"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala
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Expand Up @@ -36,8 +36,8 @@ class SamtoolsMpileupArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the samtools executable. Defaults to samtools.")
var executable: String = "samtools"

@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/samtools:1.20--h50ea8bc_0.")
var image: String = "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
@Args4jOption(required = false, name = "-docker_image", usage = "Container image to use. Defaults to quay.io/biocontainers/samtools:1.21--h50ea8bc_0.")
var image: String = "quay.io/biocontainers/samtools:1.21--h50ea8bc_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala
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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/bowtie2:2.5.2--py39h6fed5c7_0.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.2--py39h6fed5c7_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/bowtie2:2.5.2--2.5.4--h7071971_4.")
var image: String = "quay.io/biocontainers/bowtie2:2.5.4--h7071971_4"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala
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Expand Up @@ -34,8 +34,8 @@ class SingleEndStarArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the STAR-Mapper executable. Defaults to STAR.")
var executable: String = "STAR"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.10a--h9ee0642_0.")
var image: String = "quay.io/biocontainers/star:2.7.10a--h9ee0642_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.11b--h43eeafb_2.")
var image: String = "quay.io/biocontainers/star:2.7.11b--h43eeafb_2"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala
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Expand Up @@ -39,8 +39,8 @@ class SnpEffArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the SnpEff executable. Defaults to snpEff.")
var executable: String = "snpEff"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/snpeff:5.1d--hdfd78af_0.")
var image: String = "quay.io/biocontainers/snpeff:5.1d--hdfd78af_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/snpeff:5.2--hdfd78af_1.")
var image: String = "quay.io/biocontainers/snpeff:5.2--hdfd78af_1"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Star.scala
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Expand Up @@ -35,8 +35,8 @@ class StarArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the STAR-Mapper executable. Defaults to STAR.")
var executable: String = "STAR"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.10b--h9ee0642_0.")
var image: String = "quay.io/biocontainers/star:2.7.10b--h9ee0642_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/star:2.7.11b--h43eeafb_2.")
var image: String = "quay.io/biocontainers/star:2.7.11b--h43eeafb_2"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Unimap.scala
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Expand Up @@ -36,8 +36,8 @@ class UnimapArgs extends ReadGroupArgs {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Unimap executable. Defaults to unimap.")
var executable: String = "unimap"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/unimap:0.1--h7132678_2.")
var image: String = "quay.io/biocontainers/unimap:0.1--h7132678_2"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/unimap:0.1--he4a0461_4.")
var image: String = "quay.io/biocontainers/unimap:0.1--he4a0461_4"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/Vep.scala
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Expand Up @@ -39,8 +39,8 @@ class VepArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the Ensembl VEP executable. Defaults to vep.")
var executable: String = "vep"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0.")
var image: String = "quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0.")
var image: String = "quay.io/biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0"

@Args4jOption(required = false, name = "-sudo", usage = "Run via sudo.")
var sudo: Boolean = false
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4 changes: 2 additions & 2 deletions core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala
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Expand Up @@ -39,8 +39,8 @@ class VtNormalizeArgs extends Args4jBase {
@Args4jOption(required = false, name = "-executable", usage = "Path to the vt executable. Defaults to vt.")
var executable: String = "vt"

@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/vt:0.57721--h5eb663c_7.")
var image: String = "quay.io/biocontainers/vt:0.57721--h5eb663c_7"
@Args4jOption(required = false, name = "-image", usage = "Container image to use. Defaults to quay.io/biocontainers/vt:0.57721--hf74b74d_1.")
var image: String = "quay.io/biocontainers/vt:0.57721--hf74b74d_1"

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