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improvements conda #43

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merged 3 commits into from
Nov 29, 2021
Merged

improvements conda #43

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96f6bb0
improving docs
ypriverol Nov 29, 2021
b19d711
Merge remote-tracking branch 'origin/dev' into dev
ypriverol Nov 29, 2021
ccd9297
Merge branch 'bigbio:dev' into dev
ypriverol Nov 29, 2021
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3 changes: 2 additions & 1 deletion modules/local/openms/consensusid/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@ process CONSENSUSID {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/decoydatabase/main.nf
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Expand Up @@ -10,7 +10,8 @@ process DECOYDATABASE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/epifany/main.nf
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Expand Up @@ -10,7 +10,8 @@ process EPIFANY {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/extractpsmfeature/main.nf
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Expand Up @@ -11,7 +11,8 @@ process EXTRACTPSMFEATURE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/falsediscoveryrate/main.nf
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Expand Up @@ -11,7 +11,8 @@ process FALSEDISCOVERYRATE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/filemerge/main.nf
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Expand Up @@ -11,7 +11,8 @@ process FILEMERGE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/idconflictresolver/main.nf
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Expand Up @@ -10,7 +10,8 @@ process IDCONFLICTRESOLVER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/idfilter/main.nf
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Expand Up @@ -11,7 +11,8 @@ process IDFILTER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/idmapper/main.nf
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Expand Up @@ -11,7 +11,8 @@ process IDMAPPER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/idpep/main.nf
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Expand Up @@ -10,7 +10,8 @@ process IDPEP {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/idscoreswitcher/main.nf
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Expand Up @@ -12,7 +12,8 @@ process IDSCORESWITCHER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/indexpeptides/main.nf
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Expand Up @@ -10,7 +10,8 @@ process INDEXPEPTIDES {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/isobaricanalyzer/main.nf
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Expand Up @@ -12,7 +12,8 @@ process ISOBARICANALYZER {
pattern: "*.log",
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/msstatsconverter/main.nf
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Expand Up @@ -10,7 +10,8 @@ process MSSTATSCONVERTER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/mzmlindexing/main.nf
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Expand Up @@ -11,7 +11,8 @@ process MZMLINDEXING {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
// TODO Need to built single container
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
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3 changes: 2 additions & 1 deletion modules/local/openms/openmspeakpicker/main.nf
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Expand Up @@ -12,7 +12,8 @@ process OPENMSPEAKPICKER {
pattern: "*.log",
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/proteininference/main.nf
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Expand Up @@ -10,7 +10,8 @@ process PROTEININFERENCE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/proteinquantifier/main.nf
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Expand Up @@ -10,7 +10,8 @@ process PROTEINQUANTIFIER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/proteomicslfq/main.nf
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Expand Up @@ -10,7 +10,8 @@ process PROTEOMICSLFQ {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/thirdparty/luciphoradapter/main.nf
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ process LUCIPHORADAPTER {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0"
} else {
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3 changes: 2 additions & 1 deletion modules/local/openms/thirdparty/percolator/main.nf
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,8 @@ process PERCOLATOR {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::gnuplot openms::openms-thirdparty=2.7.0pre" : null)
conda (params.enable_conda ? "bioconda::bumbershoot bioconda::comet-ms bioconda::crux-toolkit=3.2 bioconda::fido=1.0 conda-forge::gnuplot bioconda::luciphor2 =2020_04_03 bioconda::msgf_plus=2021.03.22 openms::openms=2.7.0pre bioconda::pepnovo=20101117 bioconda::percolator=3.5 bioconda::sirius-csifingerid=4.0.1
bioconda::thermorawfileparser=1.3.4 bioconda::xtandem=15.12.15.2 openms::openms-thirdparty=2.7.0pre" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0"
} else {
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