diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf index 0cbe5776..0ffbc524 100644 --- a/modules/local/openms/consensusid/main.nf +++ b/modules/local/openms/consensusid/main.nf @@ -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: diff --git a/modules/local/openms/decoydatabase/main.nf b/modules/local/openms/decoydatabase/main.nf index 951725b6..8da1cebb 100644 --- a/modules/local/openms/decoydatabase/main.nf +++ b/modules/local/openms/decoydatabase/main.nf @@ -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: diff --git a/modules/local/openms/epifany/main.nf b/modules/local/openms/epifany/main.nf index 2c3ce668..0a31e263 100644 --- a/modules/local/openms/epifany/main.nf +++ b/modules/local/openms/epifany/main.nf @@ -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: diff --git a/modules/local/openms/extractpsmfeature/main.nf b/modules/local/openms/extractpsmfeature/main.nf index 096b86ae..004d8073 100644 --- a/modules/local/openms/extractpsmfeature/main.nf +++ b/modules/local/openms/extractpsmfeature/main.nf @@ -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: diff --git a/modules/local/openms/falsediscoveryrate/main.nf b/modules/local/openms/falsediscoveryrate/main.nf index 227b2115..483478af 100644 --- a/modules/local/openms/falsediscoveryrate/main.nf +++ b/modules/local/openms/falsediscoveryrate/main.nf @@ -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: diff --git a/modules/local/openms/filemerge/main.nf b/modules/local/openms/filemerge/main.nf index e42680c6..5755e814 100644 --- a/modules/local/openms/filemerge/main.nf +++ b/modules/local/openms/filemerge/main.nf @@ -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: diff --git a/modules/local/openms/idconflictresolver/main.nf b/modules/local/openms/idconflictresolver/main.nf index 364b1e9b..8f9ff17f 100644 --- a/modules/local/openms/idconflictresolver/main.nf +++ b/modules/local/openms/idconflictresolver/main.nf @@ -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: diff --git a/modules/local/openms/idfilter/main.nf b/modules/local/openms/idfilter/main.nf index a503eb6d..bc42f1b2 100644 --- a/modules/local/openms/idfilter/main.nf +++ b/modules/local/openms/idfilter/main.nf @@ -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: diff --git a/modules/local/openms/idmapper/main.nf b/modules/local/openms/idmapper/main.nf index 8008f3e6..ec9e4a71 100644 --- a/modules/local/openms/idmapper/main.nf +++ b/modules/local/openms/idmapper/main.nf @@ -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: diff --git a/modules/local/openms/idpep/main.nf b/modules/local/openms/idpep/main.nf index f50a9dc0..e16ad7f5 100644 --- a/modules/local/openms/idpep/main.nf +++ b/modules/local/openms/idpep/main.nf @@ -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: diff --git a/modules/local/openms/idscoreswitcher/main.nf b/modules/local/openms/idscoreswitcher/main.nf index bc20d415..7d1ccc3e 100644 --- a/modules/local/openms/idscoreswitcher/main.nf +++ b/modules/local/openms/idscoreswitcher/main.nf @@ -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: diff --git a/modules/local/openms/indexpeptides/main.nf b/modules/local/openms/indexpeptides/main.nf index 89d90b29..7a86a0ee 100644 --- a/modules/local/openms/indexpeptides/main.nf +++ b/modules/local/openms/indexpeptides/main.nf @@ -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: diff --git a/modules/local/openms/isobaricanalyzer/main.nf b/modules/local/openms/isobaricanalyzer/main.nf index a4b2a3ec..fde49ccb 100644 --- a/modules/local/openms/isobaricanalyzer/main.nf +++ b/modules/local/openms/isobaricanalyzer/main.nf @@ -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: diff --git a/modules/local/openms/msstatsconverter/main.nf b/modules/local/openms/msstatsconverter/main.nf index f9b5cc20..17181d68 100644 --- a/modules/local/openms/msstatsconverter/main.nf +++ b/modules/local/openms/msstatsconverter/main.nf @@ -10,11 +10,11 @@ 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 ? "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: diff --git a/modules/local/openms/mzmlindexing/main.nf b/modules/local/openms/mzmlindexing/main.nf index 43153613..c64cb19f 100644 --- a/modules/local/openms/mzmlindexing/main.nf +++ b/modules/local/openms/mzmlindexing/main.nf @@ -11,13 +11,13 @@ 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 ? "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) { // TODO Need to built single 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 { // TODO Need to built single container - container "quay.io/bigbio/quantms:dev" + container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1" } input: diff --git a/modules/local/openms/openmspeakpicker/main.nf b/modules/local/openms/openmspeakpicker/main.nf index 45198970..4ae59d91 100644 --- a/modules/local/openms/openmspeakpicker/main.nf +++ b/modules/local/openms/openmspeakpicker/main.nf @@ -12,11 +12,11 @@ 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 ? "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: diff --git a/modules/local/openms/proteininference/main.nf b/modules/local/openms/proteininference/main.nf index f3a5c40e..e88f3dd7 100644 --- a/modules/local/openms/proteininference/main.nf +++ b/modules/local/openms/proteininference/main.nf @@ -10,11 +10,11 @@ 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 ? "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: diff --git a/modules/local/openms/proteinquantifier/main.nf b/modules/local/openms/proteinquantifier/main.nf index 90706df5..f3be3e2e 100644 --- a/modules/local/openms/proteinquantifier/main.nf +++ b/modules/local/openms/proteinquantifier/main.nf @@ -10,11 +10,11 @@ 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 ? "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: diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf index 3a1aa24b..587300c4 100644 --- a/modules/local/openms/proteomicslfq/main.nf +++ b/modules/local/openms/proteomicslfq/main.nf @@ -10,11 +10,11 @@ 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 ? "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: diff --git a/modules/local/openms/thirdparty/luciphoradapter/main.nf b/modules/local/openms/thirdparty/luciphoradapter/main.nf index bcab922a..8e59d591 100644 --- a/modules/local/openms/thirdparty/luciphoradapter/main.nf +++ b/modules/local/openms/thirdparty/luciphoradapter/main.nf @@ -11,9 +11,9 @@ 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 ? "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://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0" + container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1" } else { container "quay.io/biocontainers/openms-thirdparty:2.6.0--0" } diff --git a/modules/local/openms/thirdparty/percolator/main.nf b/modules/local/openms/thirdparty/percolator/main.nf index fa66828c..4a3282b4 100644 --- a/modules/local/openms/thirdparty/percolator/main.nf +++ b/modules/local/openms/thirdparty/percolator/main.nf @@ -10,9 +10,9 @@ 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 ? "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://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0" + container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1" } else { container "quay.io/biocontainers/openms-thirdparty:2.6.0--0" } diff --git a/modules/local/openms/thirdparty/searchenginecomet/main.nf b/modules/local/openms/thirdparty/searchenginecomet/main.nf index 69a02371..99b5b94e 100644 --- a/modules/local/openms/thirdparty/searchenginecomet/main.nf +++ b/modules/local/openms/thirdparty/searchenginecomet/main.nf @@ -11,11 +11,11 @@ process SEARCHENGINECOMET { 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 ? "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://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0" + container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1" } else { - container "quay.io/biocontainers/openms-thirdparty:2.6.0--0" + container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1" } input: diff --git a/modules/local/openms/thirdparty/searchenginemsgf/main.nf b/modules/local/openms/thirdparty/searchenginemsgf/main.nf index 052d7dbf..e7dc3ee9 100644 --- a/modules/local/openms/thirdparty/searchenginemsgf/main.nf +++ b/modules/local/openms/thirdparty/searchenginemsgf/main.nf @@ -11,11 +11,11 @@ process SEARCHENGINEMSGF { 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://depot.galaxyproject.org/singularity/openms-thirdparty:2.6.0--0" + container "https://depot.galaxyproject.org/singularity/openms-thirdparty:2.7.0--h9ee0642_1" } else { - container "quay.io/biocontainers/openms-thirdparty:2.6.0--0" + container "quay.io/biocontainers/openms-thirdparty:2.7.0--h9ee0642_1" }