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Merge pull request #54 from ypriverol/dev
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openms-2.7 in bioconda
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@ypriverol
ypriverol authored Jan 10, 2022
2 parents d37fd49 + 1aa9334 commit 8222f08
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Showing 23 changed files with 67 additions and 67 deletions.
6 changes: 3 additions & 3 deletions modules/local/openms/consensusid/main.nf
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Expand Up @@ -12,11 +12,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/decoydatabase/main.nf
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Expand Up @@ -10,11 +10,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/epifany/main.nf
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Expand Up @@ -10,11 +10,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/extractpsmfeature/main.nf
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Expand Up @@ -11,11 +11,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/falsediscoveryrate/main.nf
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Expand Up @@ -11,11 +11,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/filemerge/main.nf
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Expand Up @@ -11,11 +11,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/idconflictresolver/main.nf
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Expand Up @@ -10,11 +10,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/idfilter/main.nf
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Expand Up @@ -11,11 +11,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/idmapper/main.nf
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Expand Up @@ -11,11 +11,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/idpep/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/idscoreswitcher/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/indexpeptides/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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6 changes: 3 additions & 3 deletions modules/local/openms/isobaricanalyzer/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@ 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 ? "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)
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 bioconda::openms-thirdparty=2.7.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif"
container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1"
} else {
container "quay.io/bigbio/quantms:dev"
container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1"
}

input:
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