Merge pull request #2 from bigbio/dev

u
bigbio · Nov 16, 2021 · 8d6fff3 · 8d6fff3
2 parents 1d8971e + 607169f
commit 8d6fff3
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Showing 20 changed files with 39 additions and 37 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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