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various - add build to conda definition

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This commit is contained in:
drpatelh 2021-02-03 09:20:34 +00:00
parent c0926b0b6b
commit 3ae4c51f42
13 changed files with 13 additions and 13 deletions
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2
software/qualimap/rnaseq/main.nf
View file

@ -11,7 +11,7 @@ process QUALIMAP_RNASEQ {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
conda (params.enable_conda ? "bioconda::qualimap=2.2.2d=1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
} else {

2
software/quast/main.nf
View file

@ -10,7 +10,7 @@ process QUAST {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
conda (params.enable_conda ? 'bioconda::quast=5.0.2=py37pl526hb5aa323_2' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
} else {

2
software/salmon/index/main.nf
View file

@ -11,7 +11,7 @@ process SALMON_INDEX {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
conda (params.enable_conda ? "bioconda::salmon=1.4.0=hf69c8f4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
} else {

2
software/salmon/quant/main.nf
View file

@ -11,7 +11,7 @@ process SALMON_QUANT {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
conda (params.enable_conda ? "bioconda::salmon=1.4.0=hf69c8f4_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
} else {

2
software/sortmerna/main.nf
View file

@ -11,7 +11,7 @@ process SORTMERNA {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
conda (params.enable_conda ? "bioconda::sortmerna=4.2.0=0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
} else {

2
software/star/align/main.nf
View file

@ -12,7 +12,7 @@ process STAR_ALIGN {
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? 'bioconda::star=2.6.1d' : null)
conda (params.enable_conda ? 'bioconda::star=2.6.1d=0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/star:2.6.1d--0'
} else {

2
software/star/genomegenerate/main.nf
View file

@ -12,7 +12,7 @@ process STAR_GENOMEGENERATE {
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
conda (params.enable_conda ? "bioconda::star=2.6.1d=0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
} else {

2
software/stringtie/main.nf
View file

@ -11,7 +11,7 @@ process STRINGTIE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
conda (params.enable_conda ? "bioconda::stringtie=2.1.4=h7e0af3c_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
} else {

2
software/subread/featurecounts/main.nf
View file

@ -11,7 +11,7 @@ process SUBREAD_FEATURECOUNTS {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
conda (params.enable_conda ? "bioconda::subread=2.0.1=hed695b0_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
} else {

2
software/trimgalore/main.nf
View file

@ -11,7 +11,7 @@ process TRIMGALORE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
conda (params.enable_conda ? "bioconda::trim-galore=0.6.6=0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
} else {

2
software/ucsc/bedgraphtobigwig/main.nf
View file

@ -13,7 +13,7 @@ process UCSC_BEDGRAPHTOBIGWIG {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377=h446ed27_1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
} else {

2
software/umitools/dedup/main.nf
View file

@ -11,7 +11,7 @@ process UMITOOLS_DEDUP {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1=py38h0213d0e_1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
} else {

2
software/umitools/extract/main.nf
View file

@ -11,7 +11,7 @@ process UMITOOLS_EXTRACT {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null)
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1=py38h0213d0e_1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
} else {