diff --git a/.gitignore b/.gitignore index 5124c9ac..b468c1ee 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ results/ testing/ testing* *.pyc +.idea/ +.idea/* diff --git a/modules/local/openms/consensusid/main.nf b/modules/local/openms/consensusid/main.nf index 28dc041b..f32834ec 100644 --- a/modules/local/openms/consensusid/main.nf +++ b/modules/local/openms/consensusid/main.nf @@ -14,9 +14,9 @@ process CONSENSUSID { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/decoydatabase/main.nf b/modules/local/openms/decoydatabase/main.nf index 74f3b861..6a63acba 100644 --- a/modules/local/openms/decoydatabase/main.nf +++ b/modules/local/openms/decoydatabase/main.nf @@ -12,9 +12,9 @@ process DECOYDATABASE { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/epifany/main.nf b/modules/local/openms/epifany/main.nf index 30157589..f7fadeaa 100644 --- a/modules/local/openms/epifany/main.nf +++ b/modules/local/openms/epifany/main.nf @@ -12,9 +12,9 @@ process EPIFANY { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/extractpsmfeature/main.nf b/modules/local/openms/extractpsmfeature/main.nf index 14a8b741..2b020d07 100644 --- a/modules/local/openms/extractpsmfeature/main.nf +++ b/modules/local/openms/extractpsmfeature/main.nf @@ -13,9 +13,9 @@ process EXTRACTPSMFEATURE { conda (params.enable_conda ? "bioconda::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/falsediscoveryrate/main.nf b/modules/local/openms/falsediscoveryrate/main.nf index 8ca98e27..ffd13f2a 100644 --- a/modules/local/openms/falsediscoveryrate/main.nf +++ b/modules/local/openms/falsediscoveryrate/main.nf @@ -13,9 +13,9 @@ process FALSEDISCOVERYRATE { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/filemerge/main.nf b/modules/local/openms/filemerge/main.nf index 1a675e8e..714f1682 100644 --- a/modules/local/openms/filemerge/main.nf +++ b/modules/local/openms/filemerge/main.nf @@ -13,9 +13,9 @@ process FILEMERGE { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/idconflictresolver/main.nf b/modules/local/openms/idconflictresolver/main.nf index 7543e2c2..7a0ae508 100644 --- a/modules/local/openms/idconflictresolver/main.nf +++ b/modules/local/openms/idconflictresolver/main.nf @@ -12,9 +12,9 @@ process IDCONFLICTRESOLVER { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/idfilter/main.nf b/modules/local/openms/idfilter/main.nf index d3f4cd6f..0a53292a 100644 --- a/modules/local/openms/idfilter/main.nf +++ b/modules/local/openms/idfilter/main.nf @@ -13,9 +13,9 @@ process IDFILTER { conda (params.enable_conda ? "bioconda::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/idmapper/main.nf b/modules/local/openms/idmapper/main.nf index 90ae784e..7aa692d4 100644 --- a/modules/local/openms/idmapper/main.nf +++ b/modules/local/openms/idmapper/main.nf @@ -13,9 +13,9 @@ process IDMAPPER { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/idpep/main.nf b/modules/local/openms/idpep/main.nf index c2da0e62..e67a65f1 100644 --- a/modules/local/openms/idpep/main.nf +++ b/modules/local/openms/idpep/main.nf @@ -12,9 +12,9 @@ process IDPEP { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/idscoreswitcher/main.nf b/modules/local/openms/idscoreswitcher/main.nf index 20ef64f0..b2cfbd5b 100644 --- a/modules/local/openms/idscoreswitcher/main.nf +++ b/modules/local/openms/idscoreswitcher/main.nf @@ -14,9 +14,9 @@ process IDSCORESWITCHER { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/indexpeptides/main.nf b/modules/local/openms/indexpeptides/main.nf index e8306000..94669d68 100644 --- a/modules/local/openms/indexpeptides/main.nf +++ b/modules/local/openms/indexpeptides/main.nf @@ -12,9 +12,9 @@ process INDEXPEPTIDES { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/isobaricanalyzer/main.nf b/modules/local/openms/isobaricanalyzer/main.nf index 3f702064..ed59d812 100644 --- a/modules/local/openms/isobaricanalyzer/main.nf +++ b/modules/local/openms/isobaricanalyzer/main.nf @@ -14,9 +14,9 @@ process ISOBARICANALYZER { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/msstatsconverter/main.nf b/modules/local/openms/msstatsconverter/main.nf index c068bc62..b8ddfeee 100644 --- a/modules/local/openms/msstatsconverter/main.nf +++ b/modules/local/openms/msstatsconverter/main.nf @@ -12,9 +12,9 @@ process MSSTATSCONVERTER { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/mzmlindexing/main.nf b/modules/local/openms/mzmlindexing/main.nf index cdd0a7ea..e25af5c4 100644 --- a/modules/local/openms/mzmlindexing/main.nf +++ b/modules/local/openms/mzmlindexing/main.nf @@ -15,10 +15,10 @@ process MZMLINDEXING { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { // TODO Need to built single container - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { // TODO Need to built single container - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/openmspeakpicker/main.nf b/modules/local/openms/openmspeakpicker/main.nf index a5df175d..e9ac3114 100644 --- a/modules/local/openms/openmspeakpicker/main.nf +++ b/modules/local/openms/openmspeakpicker/main.nf @@ -14,9 +14,9 @@ process OPENMSPEAKPICKER { conda (params.enable_conda ? "openms::openms-thirdparty=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/proteininference/main.nf b/modules/local/openms/proteininference/main.nf index 4a03682a..65f1b91d 100644 --- a/modules/local/openms/proteininference/main.nf +++ b/modules/local/openms/proteininference/main.nf @@ -12,9 +12,9 @@ process PROTEININFERENCE { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/modules/local/openms/proteinquantifier/main.nf b/modules/local/openms/proteinquantifier/main.nf index 68051b46..1fab5c4f 100644 --- a/modules/local/openms/proteinquantifier/main.nf +++ b/modules/local/openms/proteinquantifier/main.nf @@ -12,9 +12,9 @@ process PROTEINQUANTIFIER { conda (params.enable_conda ? "openms::openms=2.7.0pre" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/openms:2.6.0--h4afb90d_0" + container "https://ftp.pride.ebi.ac.uk/pride/data/tools/quantms-dev.sif" } else { - container "quay.io/biocontainers/openms:2.6.0--h4afb90d_0" + container "quay.io/bigbio/quantms:dev" } input: diff --git a/nextflow.config b/nextflow.config index 094d2f3e..1c5696db 100644 --- a/nextflow.config +++ b/nextflow.config @@ -113,7 +113,7 @@ params { greedy_group_resolution = 'none' // Epifany - protein_inference_bayesian = true + protein_inference_bayesian = false greedy_group_resolution = 'none' top_PSMs = 1 update_PSM_probabilities = true