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various - add build to conda definition

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drpatelh 2021-02-03 09:19:46 +00:00
parent daab19a849
commit c0926b0b6b
13 changed files with 13 additions and 13 deletions
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2
software/dsh/filterbed/main.nf
View file

@ -11,7 +11,7 @@ process DSH_FILTERBED {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::dsh-bio=2.0" : null) conda (params.enable_conda ? "bioconda::dsh-bio=2.0=0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0--0" container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0--0"
} else { } else {

2
software/dsh/splitbed/main.nf
View file

@ -11,7 +11,7 @@ process DSH_SPLITBED {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::dsh-bio=2.0" : null) conda (params.enable_conda ? "bioconda::dsh-bio=2.0=0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0--0" container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0--0"
} else { } else {

2
software/fastp/main.nf
View file

@ -11,7 +11,7 @@ process FASTP {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null) conda (params.enable_conda ? 'bioconda::fastp=0.20.1=h8b12597_0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' container 'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0'
} else { } else {

2
software/fastqc/main.nf
View file

@ -11,7 +11,7 @@ process FASTQC {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) conda (params.enable_conda ? "bioconda::fastqc=0.11.9=0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0" container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
} else { } else {

2
software/gffread/main.nf
View file

@ -10,7 +10,7 @@ process GFFREAD {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) conda (params.enable_conda ? "bioconda::gffread=0.12.1=h8b12597_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0" container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
} else { } else {

2
software/hisat2/build/main.nf
View file

@ -12,7 +12,7 @@ process HISAT2_BUILD {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null) conda (params.enable_conda ? "bioconda::hisat2=2.2.0=py37hfa133b6_4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4" container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
} else { } else {

2
software/hisat2/extractsplicesites/main.nf
View file

@ -11,7 +11,7 @@ process HISAT2_EXTRACTSPLICESITES {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null) conda (params.enable_conda ? "bioconda::hisat2=2.2.0=py37hfa133b6_4" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4" container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
} else { } else {

2
software/homer/annotatepeaks/main.nf
View file

@ -13,7 +13,7 @@ process HOMER_ANNOTATEPEAKS {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::homer=4.11" : null) conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3" container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
} else { } else {

2
software/macs2/callpeak/main.nf
View file

@ -11,7 +11,7 @@ process MACS2_CALLPEAK {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) conda (params.enable_conda ? "bioconda::macs2=2.2.7.1=py38h0213d0e_1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1" container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1"
} else { } else {

2
software/multiqc/main.nf
View file

@ -10,7 +10,7 @@ process MULTIQC {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: '') } saveAs: { filename -> saveFiles(filename: filename, options: params.options, publish_dir: getSoftwareName(task.process), publish_id: '') }
conda (params.enable_conda ? "bioconda::multiqc=1.9" : null) conda (params.enable_conda ? "bioconda::multiqc=1.9=pyh9f0ad1d_0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0" container "https://depot.galaxyproject.org/singularity/multiqc:1.9--pyh9f0ad1d_0"
} else { } else {

2
software/pangolin/main.nf
View file

@ -11,7 +11,7 @@ process PANGOLIN {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? 'bioconda::pangolin=2.1.7' : null) conda (params.enable_conda ? 'bioconda::pangolin=2.1.7=py_0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/pangolin:2.1.7--py_0' container 'https://depot.galaxyproject.org/singularity/pangolin:2.1.7--py_0'
} else { } else {

2
software/phantompeakqualtools/main.nf
View file

@ -13,7 +13,7 @@ process PHANTOMPEAKQUALTOOLS {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null) conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2=0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0" container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
} else { } else {

2
software/preseq/lcextrap/main.nf
View file

@ -12,7 +12,7 @@ process PRESEQ_LCEXTRAP {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null) conda (params.enable_conda ? "bioconda::preseq=2.0.3=hf53bd2b_3" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3" container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
} else { } else {