From 4085296bf221c834a2298892dca2c757db5eb25e Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Sun, 17 Nov 2024 09:28:23 +0000
Subject: [PATCH 01/24] remove big-nodes.config

---
 conf/dev.config | 2 +-
 nextflow.config | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/dev.config b/conf/dev.config
index 45a8f34d..4a2058ec 100644
--- a/conf/dev.config
+++ b/conf/dev.config
@@ -18,7 +18,7 @@ params {
 
 process {
     withLabel: openms {
-        conda = "openms::openms-thirdparty=3.2.0"
+        conda = "bioconda::openms-thirdparty=3.2.0" // The conda package is not the nightly version
         container = {"${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'ghcr.io/openms/openms-executables-sif:latest' : 'ghcr.io/openms/openms-executables:latest' }"}
     }
 }
diff --git a/nextflow.config b/nextflow.config
index ec761e09..6bbc5d31 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -406,6 +406,7 @@ profiles {
     test_full       { includeConfig 'conf/test_full_lfq.config'   }
     test_dda_id     { includeConfig 'conf/test_dda_id.config'     }
     mambaci         { includeConfig 'conf/mambaci.config'         }
+    dev             { includeConfig 'conf/dev.config'             }
 }
 
 // Load nf-core custom profiles from different Institutions

From db259e8edf6b686409277cb81d8b7c51d60d6022 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Sun, 17 Nov 2024 12:51:28 +0000
Subject: [PATCH 02/24] move diann 1.9.1beta to config

---
 conf/test_latest_dia.config                      | 5 +++++
 modules/local/assemble_empirical_library/main.nf | 5 +----
 modules/local/diann_preliminary_analysis/main.nf | 5 +----
 modules/local/diannsummary/main.nf               | 5 +----
 modules/local/individual_final_analysis/main.nf  | 5 +----
 modules/local/silicolibrarygeneration/main.nf    | 5 +----
 6 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config
index ab99bf59..0e46589a 100644
--- a/conf/test_latest_dia.config
+++ b/conf/test_latest_dia.config
@@ -47,5 +47,10 @@ process {
     withName: 'NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER' {
         publishDir  = [path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" }, pattern: "*.log" ]
     }
+
+    withLabel: diann {
+        container = 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
+        singularity.enabled = true
+    }
 }
 
diff --git a/modules/local/assemble_empirical_library/main.nf b/modules/local/assemble_empirical_library/main.nf
index 2aa1d9d5..9045e285 100644
--- a/modules/local/assemble_empirical_library/main.nf
+++ b/modules/local/assemble_empirical_library/main.nf
@@ -1,15 +1,12 @@
 process ASSEMBLE_EMPIRICAL_LIBRARY {
     tag "$meta.experiment_id"
     label 'process_low'
+    label 'diann'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
         'docker.io/biocontainers/diann:v1.8.1_cv1' }"
 
-    if (params.diann_version == "1.9.beta.1") {
-        container 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
-    }
-
     input:
     // In this step the real files are passed, and not the names
     path(ms_files)
diff --git a/modules/local/diann_preliminary_analysis/main.nf b/modules/local/diann_preliminary_analysis/main.nf
index 01699a93..c8ad0faf 100644
--- a/modules/local/diann_preliminary_analysis/main.nf
+++ b/modules/local/diann_preliminary_analysis/main.nf
@@ -1,15 +1,12 @@
 process DIANN_PRELIMINARY_ANALYSIS {
     tag "$ms_file.baseName"
     label 'process_high'
+    label 'diann'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
         'docker.io/biocontainers/diann:v1.8.1_cv1' }"
 
-    if (params.diann_version == "1.9.beta.1") {
-        container 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
-    }
-
     input:
     tuple val(meta), path(ms_file), path(predict_library)
 
diff --git a/modules/local/diannsummary/main.nf b/modules/local/diannsummary/main.nf
index c8547691..4572c3d0 100644
--- a/modules/local/diannsummary/main.nf
+++ b/modules/local/diannsummary/main.nf
@@ -1,15 +1,12 @@
 process DIANNSUMMARY {
     tag "$meta.experiment_id"
     label 'process_high'
+    label 'diann'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
         'docker.io/biocontainers/diann:v1.8.1_cv1' }"
 
-    if (params.diann_version == "1.9.beta.1") {
-        container 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
-    }
-
     input:
     // Note that the files are passed as names and not paths, this prevents them from being staged
     // in the directory
diff --git a/modules/local/individual_final_analysis/main.nf b/modules/local/individual_final_analysis/main.nf
index 35efa3da..8e2e3c46 100644
--- a/modules/local/individual_final_analysis/main.nf
+++ b/modules/local/individual_final_analysis/main.nf
@@ -1,15 +1,12 @@
 process INDIVIDUAL_FINAL_ANALYSIS {
     tag "$ms_file.baseName"
     label 'process_high'
+    label 'diann'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
         'docker.io/biocontainers/diann:v1.8.1_cv1' }"
 
-    if (params.diann_version == "1.9.beta.1") {
-        container 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
-    }
-
     input:
     tuple val(meta), path(ms_file), path(fasta), path(diann_log), path(library)
 
diff --git a/modules/local/silicolibrarygeneration/main.nf b/modules/local/silicolibrarygeneration/main.nf
index 50b16e78..e134a31e 100644
--- a/modules/local/silicolibrarygeneration/main.nf
+++ b/modules/local/silicolibrarygeneration/main.nf
@@ -1,15 +1,12 @@
 process SILICOLIBRARYGENERATION {
     tag "$fasta.Name"
     label 'process_medium'
+    label 'diann'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
         'docker.io/biocontainers/diann:v1.8.1_cv1' }"
 
-    if (params.diann_version == "1.9.beta.1") {
-        container 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
-    }
-
     input:
     file(fasta)
     file(diann_config)

From 78d35e9e036a5652424660f5c3e6edd7dd372ee3 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Sun, 17 Nov 2024 19:29:57 +0000
Subject: [PATCH 03/24] quantms-utils 0.0.11 -> 0.0.12

---
 modules/local/add_sage_feat/main.nf      | 6 +++---
 modules/local/diannconvert/main.nf       | 6 +++---
 modules/local/extract_psm/main.nf        | 6 +++---
 modules/local/extract_sample/main.nf     | 6 +++---
 modules/local/generate_diann_cfg/main.nf | 6 +++---
 modules/local/ms2rescore/main.nf         | 6 +++---
 modules/local/mzmlstatistics/main.nf     | 6 +++---
 modules/local/preprocess_expdesign.nf    | 2 +-
 modules/local/samplesheet_check.nf       | 2 +-
 modules/local/sdrfparsing/main.nf        | 6 +++---
 modules/local/spectrum2features/main.nf  | 6 +++---
 11 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf
index ce7f53db..395807d4 100644
--- a/modules/local/add_sage_feat/main.nf
+++ b/modules/local/add_sage_feat/main.nf
@@ -2,10 +2,10 @@ process SAGEFEATURE {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(extra_feat)
diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf
index 40b273b1..9e2f9e8b 100644
--- a/modules/local/diannconvert/main.nf
+++ b/modules/local/diannconvert/main.nf
@@ -2,10 +2,10 @@ process DIANNCONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
     input:
     path(report)
diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf
index ce166ae3..af69fc82 100644
--- a/modules/local/extract_psm/main.nf
+++ b/modules/local/extract_psm/main.nf
@@ -2,10 +2,10 @@ process PSMCONVERSION {
     tag "$meta.mzml_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf
index da5dd5b7..359b88dc 100644
--- a/modules/local/extract_sample/main.nf
+++ b/modules/local/extract_sample/main.nf
@@ -2,10 +2,10 @@ process GETSAMPLE {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf
index 3e4b5a91..4a66bf8a 100644
--- a/modules/local/generate_diann_cfg/main.nf
+++ b/modules/local/generate_diann_cfg/main.nf
@@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG {
     tag "$meta.experiment_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
     input:
     val(meta)
diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf
index efd208d6..91a19f3e 100644
--- a/modules/local/ms2rescore/main.nf
+++ b/modules/local/ms2rescore/main.nf
@@ -2,10 +2,10 @@ process MS2RESCORE {
     tag "$meta.mzml_id"
     label 'process_high'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
     // userEmulation settings when docker is specified
     containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf
index da83cb40..51685bff 100644
--- a/modules/local/mzmlstatistics/main.nf
+++ b/modules/local/mzmlstatistics/main.nf
@@ -3,10 +3,10 @@ process MZMLSTATISTICS {
     label 'process_very_low'
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ms_file)
diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
index 11114c0a..ceb79362 100644
--- a/modules/local/preprocess_expdesign.nf
+++ b/modules/local/preprocess_expdesign.nf
@@ -6,7 +6,7 @@ process PREPROCESS_EXPDESIGN {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
         'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 7fd66925..0749ef1c 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -3,7 +3,7 @@ process SAMPLESHEET_CHECK {
     tag "$input_file"
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
         'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
index 53899f0b..2ac0427e 100644
--- a/modules/local/sdrfparsing/main.nf
+++ b/modules/local/sdrfparsing/main.nf
@@ -2,10 +2,10 @@ process SDRFPARSING {
     tag "$sdrf.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
     input:
     path sdrf
diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf
index 7deaf981..9edce8a8 100644
--- a/modules/local/spectrum2features/main.nf
+++ b/modules/local/spectrum2features/main.nf
@@ -2,10 +2,10 @@ process SPECTRUM2FEATURES {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.11"
+    conda "bioconda::quantms-utils=0.0.12"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.11--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(ms_file)

From d9f9fe2144de50340a8f4463238c8a4342673110 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 09:24:08 +0000
Subject: [PATCH 04/24] remove diann version

---
 conf/test_latest_dia.config                | 1 -
 nextflow.config                            | 1 -
 nextflow_schema.json                       | 6 ------
 subworkflows/local/create_input_channel.nf | 3 ---
 4 files changed, 11 deletions(-)

diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config
index 0e46589a..4e36967e 100644
--- a/conf/test_latest_dia.config
+++ b/conf/test_latest_dia.config
@@ -27,7 +27,6 @@ params {
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/dia_ci/PXD026600.sdrf.tsv'
     database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/dia_ci/REF_EColi_K12_UPS1_combined.fasta'
-    diann_version = '1.9.beta.1'
     min_pr_mz = 350
     max_pr_mz = 950
     min_fr_mz = 500
diff --git a/nextflow.config b/nextflow.config
index 6bbc5d31..78bbf2f4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -189,7 +189,6 @@ params {
     convert_dotd            = false
 
     // DIA-NN
-    diann_version           = '1.8.1'  // Possible versions are '1.8.1', '1.9.beta.1'
     diann_debug             = 3
     scan_window             = 8
     scan_window_automatic   = true
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 59722a71..626ba6fb 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1005,12 +1005,6 @@
             "description": "Settings for DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing.",
             "default": "",
             "properties": {
-                "diann_version": {
-                    "type": "string",
-                    "description": "The version of DIA-NN used",
-                    "fa_icon": "fas fa-font",
-                    "help_text": "There are differences between the different DIA-NN versions. DIA-NN do not support cloud freely in 1.9.beta.1"
-                },
                 "mass_acc_automatic": {
                     "type": "boolean",
                     "default": true,
diff --git a/subworkflows/local/create_input_channel.nf b/subworkflows/local/create_input_channel.nf
index 0c25ecfb..190a8f56 100644
--- a/subworkflows/local/create_input_channel.nf
+++ b/subworkflows/local/create_input_channel.nf
@@ -168,9 +168,6 @@ def create_meta_channel(LinkedHashMap row, is_sdrf, enzymes, files, wrapper) {
     } else if (session.config.conda && session.config.conda.enabled) {
         log.error "File in DIA mode found in input design and conda profile was chosen. DIA-NN currently doesn't support conda! Exiting. Please use the docker/singularity profile with a container."
         exit 1
-    } else if (!session.config.singularity.enabled && params.diann_version == "1.9.beta.1") {
-        log.error "DIA-NN 1.9.beta.1 currently only support singularity! Exiting. Please use the singularity profile with a container."
-        exit 1
     }
 
     if (wrapper.labelling_type.contains("label free") || meta.acquisition_method == "dia") {

From 6e4ef563e0d17337d72109a6eff6ce196cd44b6c Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 09:40:06 +0000
Subject: [PATCH 05/24] pride slurm added

---
 conf/pride_codon_slurm.config | 60 +++++++++++++++++++++++++++++++++++
 nextflow.config               |  9 +-----
 2 files changed, 61 insertions(+), 8 deletions(-)
 create mode 100644 conf/pride_codon_slurm.config

diff --git a/conf/pride_codon_slurm.config b/conf/pride_codon_slurm.config
new file mode 100644
index 00000000..8496ae15
--- /dev/null
+++ b/conf/pride_codon_slurm.config
@@ -0,0 +1,60 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Nextflow config file for EMBL-EBI Codon Cluster for the SLURM login nodes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Author: Yasset Perez-Riverol
+Mail: yperez@ebi.ac.uk
+URL: https://www.ebi.ac.uk/
+Basedon: https://github.com/nf-core/configs/blob/master/conf/ebi_codon_slurm.config
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    config_profile_contact     = "Yasset Perez-Riverol"
+    config_profile_description = "The European Bioinformatics Institute HPC cluster (codon) profile for the SLURM login nodes"
+    config_profile_url         = "https://www.ebi.ac.uk/"
+}
+
+singularity {
+    enabled     = true
+    // the default is 20 minutes and fails with large images
+    pullTimeout = "3 hours"
+    autoMounts = false
+    runOptions = '-B /hps/nobackup/juan/pride/reanalysis:/hps/nobackup/juan/pride/reanalysis'
+    cacheDir = "/hps/nobackup/juan/pride/reanalysis/singularity/"
+}
+
+process {
+    // this is to avoid errors for missing files due to shared filesystem latency
+    maxRetries    = 30
+    errorStrategy = { task.exitStatus == 0 ? "retry" : "terminate" }
+    cache         = "lenient"
+    afterScript   = "sleep 60"
+
+    withName:PROTEOMICSLFQ{
+      memory = {(mzmls as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt }
+      cpus   = {(mzmls as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt }
+    }
+
+    withName:ASSEMBLE_EMPIRICAL_LIBRARY{
+      memory = {(ms_files as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt}
+      cpus   = {(ms_files as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt }
+    }
+
+    withLabel: diann {
+        container = 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
+    }
+}
+
+executor {
+    name            = "slurm"
+    queueSize       = 2000
+    submitRateLimit = "10/1sec"
+    exitReadTimeout = "30 min"
+    jobName         = {
+        task.name
+            .replace("[", "(")
+            .replace("]", ")")
+            .replace(" ", "_")
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index 78bbf2f4..da851742 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -383,14 +383,6 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
     }
-    ebicluster {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        conda.createTimeout    = '1 h'
-        conda.useMamba         = true
-        process.executor       = 'lsf'
-    }
     test            { includeConfig 'conf/test_lfq.config'        }
     test_localize   { includeConfig 'conf/test_localize.config'   }
     test_tmt        { includeConfig 'conf/test_tmt.config'        }
@@ -406,6 +398,7 @@ profiles {
     test_dda_id     { includeConfig 'conf/test_dda_id.config'     }
     mambaci         { includeConfig 'conf/mambaci.config'         }
     dev             { includeConfig 'conf/dev.config'             }
+    pride_slurm     { includeConfig 'conf/pride_codon_slurm.config' }
 }
 
 // Load nf-core custom profiles from different Institutions

From 4b4aff0cb219c058b0e6ab26f4ed10fbba5d8672 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 09:48:42 +0000
Subject: [PATCH 06/24] pride slurm added

---
 conf/pride_codon_slurm.config | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/conf/pride_codon_slurm.config b/conf/pride_codon_slurm.config
index 8496ae15..a9b4d7d9 100644
--- a/conf/pride_codon_slurm.config
+++ b/conf/pride_codon_slurm.config
@@ -32,13 +32,13 @@ process {
     afterScript   = "sleep 60"
 
     withName:PROTEOMICSLFQ{
-      memory = {(mzmls as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt }
-      cpus   = {(mzmls as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt }
+        memory = {(mzmls as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt }
+        cpus   = {(mzmls as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt }
     }
 
     withName:ASSEMBLE_EMPIRICAL_LIBRARY{
-      memory = {(ms_files as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt}
-      cpus   = {(ms_files as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt }
+        memory = {(ms_files as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt}
+        cpus   = {(ms_files as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt }
     }
 
     withLabel: diann {

From 26eb83f9ebb12851feec860af8a684bc87676784 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 11:07:37 +0000
Subject: [PATCH 07/24] diann 1.9.1dev -> 1.9.2

---
 conf/test_latest_dia.config | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config
index 4e36967e..9a6796c0 100644
--- a/conf/test_latest_dia.config
+++ b/conf/test_latest_dia.config
@@ -48,8 +48,9 @@ process {
     }
 
     withLabel: diann {
-        container = 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
-        singularity.enabled = true
+        container = 'ghcr.io/bigbio/diann:1.9.2' // This docker container is private in for quantms
+        docker.enabled = true
+        singularity.enabled = false
     }
 }
 

From a8143557c56ece9792bcae873d86d23beaa80597 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 11:26:32 +0000
Subject: [PATCH 08/24] diann 1.9.1dev -> 1.9.2

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b46e6f26..4d2957b5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -49,7 +49,7 @@ jobs:
             exec_profile: "conda"
         include:
           - test_profile: test_latest_dia
-            exec_profile: "singularity"
+            exec_profile: "docker"
           - test_profile: test_lfq
             exec_profile: "conda"
           - test_profile: test_dda_id

From a0bad9efcb14a4071de7701a8115674f8bae5f49 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 11:43:09 +0000
Subject: [PATCH 09/24] diann 1.9.1dev -> 1.9.2

---
 conf/test_latest_dia.config | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/conf/test_latest_dia.config b/conf/test_latest_dia.config
index 9a6796c0..7ec11563 100644
--- a/conf/test_latest_dia.config
+++ b/conf/test_latest_dia.config
@@ -10,14 +10,6 @@
 ------------------------------------------------------------------------------------------------
 */
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '12.GB',
-        time: '48.h'
-    ]
-}
-
 params {
     config_profile_name        = 'Test profile for latest DIA'
     config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch for latest DIA-NN.'
@@ -49,8 +41,16 @@ process {
 
     withLabel: diann {
         container = 'ghcr.io/bigbio/diann:1.9.2' // This docker container is private in for quantms
-        docker.enabled = true
-        singularity.enabled = false
     }
+
+    resourceLimits = [
+        cpus: 4,
+        memory: '12.GB',
+        time: '48.h'
+    ]
+
 }
 
+singularity.enabled = false // Force to use docker
+docker.enabled = true
+

From 2c2380af045edc3d95d85fb29aec64840869fb74 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 13:53:44 +0000
Subject: [PATCH 10/24] private containers login

---
 .github/workflows/ci.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4d2957b5..b09fb173 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -67,6 +67,13 @@ jobs:
         if: matrix.exec_profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
+      - name: Log in to the Container registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_TOKEN }}
+
       - name: Set up Singularity
         if: matrix.exec_profile == 'singularity'
         run: |

From 7ea1f4c00faba63c2bb28f4e219ece5d08eaba34 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 13:56:26 +0000
Subject: [PATCH 11/24] private containers login

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b09fb173..240075a3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -68,7 +68,7 @@ jobs:
         uses: eWaterCycle/setup-apptainer@main
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ secrets.GHCR_USERNAME }}

From 4512b410ab70bdf451ee80000165b01d484f2026 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 14:19:09 +0000
Subject: [PATCH 12/24] private containers login

---
 .github/workflows/ci.yml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 240075a3..6bcfc395 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -67,12 +67,9 @@ jobs:
         if: matrix.exec_profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
-      - name: Log in to the Container registry
-        uses: docker/login-action@v3
-        with:
-          registry: ghcr.io
-          username: ${{ secrets.GHCR_USERNAME }}
-          password: ${{ secrets.GHCR_TOKEN }}
+      - name: Log in to GitHub Container Registry
+        run: echo "${{ secrets.GHCR_TOKEN }}" | docker login ghcr.io -u "${{ secrets.GHCR_USERNAME }}" --password
+
 
       - name: Set up Singularity
         if: matrix.exec_profile == 'singularity'

From 70ce58eb4d8793d14daded8e5a8b173101d2a19e Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 14:34:20 +0000
Subject: [PATCH 13/24] private containers login

---
 .github/workflows/ci.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6bcfc395..01982ea0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -5,6 +5,10 @@ on:
     branches:
       - dev
   pull_request:
+  pull_request_target:
+    types:
+      - opened
+      - synchronize
   release:
     types: [published]
   workflow_dispatch:
@@ -68,8 +72,11 @@ jobs:
         uses: eWaterCycle/setup-apptainer@main
 
       - name: Log in to GitHub Container Registry
-        run: echo "${{ secrets.GHCR_TOKEN }}" | docker login ghcr.io -u "${{ secrets.GHCR_USERNAME }}" --password
-
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_TOKEN }}
 
       - name: Set up Singularity
         if: matrix.exec_profile == 'singularity'

From 2c1829c829758cb0cfb61cae31f0433c734ded6b Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 14:38:16 +0000
Subject: [PATCH 14/24] private containers login

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 01982ea0..14258f38 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - dev
-  pull_request:
   pull_request_target:
     types:
       - opened

From 5d773772ee8448fa0ab544625cb6cbe73c63a63c Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 14:45:49 +0000
Subject: [PATCH 15/24] private containers login

---
 .github/workflows/ci.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 14258f38..e7e6d9bb 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -4,7 +4,12 @@ on:
   push:
     branches:
       - dev
+  pull_request:
+    branches:
+      - dev
   pull_request_target:
+    branches:
+      - dev
     types:
       - opened
       - synchronize
@@ -70,6 +75,11 @@ jobs:
         if: matrix.exec_profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
+      - name: Run sensitive task
+        if: github.event.pull_request.base.ref == 'main'
+        run: |
+          echo "Running task with secrets."
+
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3
         with:

From a626a2a872d908a403ad8c169fc779394f0e5a20 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 14:58:56 +0000
Subject: [PATCH 16/24] private containers login

---
 .github/workflows/ci.yml | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e7e6d9bb..5fd09063 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -5,14 +5,6 @@ on:
     branches:
       - dev
   pull_request:
-    branches:
-      - dev
-  pull_request_target:
-    branches:
-      - dev
-    types:
-      - opened
-      - synchronize
   release:
     types: [published]
   workflow_dispatch:
@@ -56,8 +48,6 @@ jobs:
           - NXF_VER: "latest-everything"
             exec_profile: "conda"
         include:
-          - test_profile: test_latest_dia
-            exec_profile: "docker"
           - test_profile: test_lfq
             exec_profile: "conda"
           - test_profile: test_dda_id
@@ -75,18 +65,6 @@ jobs:
         if: matrix.exec_profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
-      - name: Run sensitive task
-        if: github.event.pull_request.base.ref == 'main'
-        run: |
-          echo "Running task with secrets."
-
-      - name: Log in to GitHub Container Registry
-        uses: docker/login-action@v3
-        with:
-          registry: ghcr.io
-          username: ${{ secrets.GHCR_USERNAME }}
-          password: ${{ secrets.GHCR_TOKEN }}
-
       - name: Set up Singularity
         if: matrix.exec_profile == 'singularity'
         run: |

From c328512bee984bfc543b135860b8c62fd8374bf1 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 15:04:56 +0000
Subject: [PATCH 17/24] add diann_private.yml

---
 .github/workflows/diann_private.yml | 86 +++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100644 .github/workflows/diann_private.yml

diff --git a/.github/workflows/diann_private.yml b/.github/workflows/diann_private.yml
new file mode 100644
index 00000000..ef724245
--- /dev/null
+++ b/.github/workflows/diann_private.yml
@@ -0,0 +1,86 @@
+name: Fork-specific CI for test_latest_dia
+
+# Trigger only for your fork and the 'test_latest_dia' test profile
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+    branches:
+      - dev
+    paths:
+      - "**.yml"
+
+env:
+  NXF_ANSI_LOG: false
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Run test_latest_dia with Docker
+    runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+      CAPSULE_LOG: none
+      TEST_PROFILE: test_latest_dia
+      EXEC_PROFILE: docker
+
+    # Ensure this workflow only runs for your fork
+    if: ${{ github.repository == 'ypriverol/quantms' }}
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v4
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "24.04.2"  # Or the Nextflow version you prefer
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_TOKEN }}
+
+      - name: Run test_latest_dia with Docker
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
+
+      - name: Gather failed logs
+        if: failure() || cancelled()
+        run: |
+          mkdir failed_logs
+          failed=$(grep "FAILED" ${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt | cut -f 2)
+          while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed"
+
+      - uses: actions/upload-artifact@v4
+        if: failure() || cancelled()
+        name: Upload failed logs
+        with:
+          name: failed_logs_${{ matrix.test_profile }}_${{ matrix.exec_profile }}
+          include-hidden-files: true
+          path: failed_logs
+          overwrite: false
+
+      - uses: actions/upload-artifact@v4
+        if: always()
+        name: Upload results
+        with:
+          name: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results
+          include-hidden-files: true
+          path: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results
+          overwrite: false
+
+      - uses: actions/upload-artifact@v4
+        if: always()
+        name: Upload log
+        with:
+          name: nextflow_${{ matrix.test_profile }}_${{ matrix.exec_profile }}.log
+          include-hidden-files: true
+          path: .nextflow.log
+          overwrite: false

From 82c6318c7cfa267063176bd657c9871c7845616e Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 15:26:47 +0000
Subject: [PATCH 18/24] add diann_private.yml

---
 .github/workflows/diann_private.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/diann_private.yml b/.github/workflows/diann_private.yml
index ef724245..d5b7619b 100644
--- a/.github/workflows/diann_private.yml
+++ b/.github/workflows/diann_private.yml
@@ -38,7 +38,7 @@ jobs:
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
-          version: "24.04.2"  # Or the Nextflow version you prefer
+          version: "24.04.2" # Or the Nextflow version you prefer
 
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3

From 3f2dce53006e1895cc986926e176b2ad4a38e8f8 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 18 Nov 2024 19:29:50 +0000
Subject: [PATCH 19/24] add diann_private.yml

---
 workflows/dia.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/workflows/dia.nf b/workflows/dia.nf
index d7a62dae..7e07cfb2 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -44,8 +44,7 @@ workflow DIA {
         result ->
         meta:   preprocessed_meta(result[0])
         ms_file:result[1]
-    }
-        .set { ch_result }
+    }.set { ch_result }
 
     meta = ch_result.meta.unique { it[0] }
 
@@ -69,7 +68,6 @@ workflow DIA {
         indiv_fin_analysis_in = ch_file_preparation_results.combine(ch_searchdb)
             .combine(assembly_log)
             .combine(empirical_library)
-
         empirical_lib = empirical_library
     } else {
         //

From 9e0487a947e9f391f3f79140ce254c4bd91ce79c Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Tue, 19 Nov 2024 19:06:25 +0800
Subject: [PATCH 20/24] compatible with different formats

---
 modules/local/assemble_empirical_library/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/assemble_empirical_library/main.nf b/modules/local/assemble_empirical_library/main.nf
index 9045e285..93c08219 100644
--- a/modules/local/assemble_empirical_library/main.nf
+++ b/modules/local/assemble_empirical_library/main.nf
@@ -15,7 +15,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     path(lib)
 
     output:
-    path "empirical_library.tsv", emit: empirical_library
+    path "empirical_library.*", emit: empirical_library
     path "assemble_empirical_library.log", emit: log
     path "versions.yml", emit: versions
 
@@ -45,7 +45,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     diann   --f ${(ms_files as List).join(' --f ')} \\
             --lib ${lib} \\
             --threads ${task.cpus} \\
-            --out-lib empirical_library.tsv \\
+            --out-lib empirical_library \\
             --verbose $params.diann_debug \\
             --rt-profiling \\
             --temp ./quant/ \\

From 440a182ebd809e71a5471d5d8c6b9d744c2ef509 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Thu, 21 Nov 2024 09:02:24 +0000
Subject: [PATCH 21/24] quantms-utils 0.0.12 -> 0.0.13

---
 modules/local/add_sage_feat/main.nf      | 6 +++---
 modules/local/diannconvert/main.nf       | 6 +++---
 modules/local/extract_psm/main.nf        | 6 +++---
 modules/local/extract_sample/main.nf     | 6 +++---
 modules/local/generate_diann_cfg/main.nf | 6 +++---
 modules/local/ms2rescore/main.nf         | 6 +++---
 modules/local/mzmlstatistics/main.nf     | 6 +++---
 modules/local/preprocess_expdesign.nf    | 6 +++---
 modules/local/samplesheet_check.nf       | 6 +++---
 modules/local/sdrfparsing/main.nf        | 6 +++---
 modules/local/spectrum2features/main.nf  | 6 +++---
 11 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf
index 395807d4..052cc0b5 100644
--- a/modules/local/add_sage_feat/main.nf
+++ b/modules/local/add_sage_feat/main.nf
@@ -2,10 +2,10 @@ process SAGEFEATURE {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(extra_feat)
diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf
index 9e2f9e8b..9608b918 100644
--- a/modules/local/diannconvert/main.nf
+++ b/modules/local/diannconvert/main.nf
@@ -2,10 +2,10 @@ process DIANNCONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     path(report)
diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf
index af69fc82..e6c884b9 100644
--- a/modules/local/extract_psm/main.nf
+++ b/modules/local/extract_psm/main.nf
@@ -2,10 +2,10 @@ process PSMCONVERSION {
     tag "$meta.mzml_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf
index 359b88dc..f14e7693 100644
--- a/modules/local/extract_sample/main.nf
+++ b/modules/local/extract_sample/main.nf
@@ -2,10 +2,10 @@ process GETSAMPLE {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf
index 4a66bf8a..afd6123e 100644
--- a/modules/local/generate_diann_cfg/main.nf
+++ b/modules/local/generate_diann_cfg/main.nf
@@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG {
     tag "$meta.experiment_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     val(meta)
diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf
index 91a19f3e..228d7529 100644
--- a/modules/local/ms2rescore/main.nf
+++ b/modules/local/ms2rescore/main.nf
@@ -2,10 +2,10 @@ process MS2RESCORE {
     tag "$meta.mzml_id"
     label 'process_high'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     // userEmulation settings when docker is specified
     containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf
index 51685bff..5ecb0958 100644
--- a/modules/local/mzmlstatistics/main.nf
+++ b/modules/local/mzmlstatistics/main.nf
@@ -3,10 +3,10 @@ process MZMLSTATISTICS {
     label 'process_very_low'
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ms_file)
diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
index ceb79362..e9d66cf8 100644
--- a/modules/local/preprocess_expdesign.nf
+++ b/modules/local/preprocess_expdesign.nf
@@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     path design
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 0749ef1c..6839b550 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
     tag "$input_file"
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     path input_file
diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
index 2ac0427e..8a26586b 100644
--- a/modules/local/sdrfparsing/main.nf
+++ b/modules/local/sdrfparsing/main.nf
@@ -2,10 +2,10 @@ process SDRFPARSING {
     tag "$sdrf.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     path sdrf
diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf
index 9edce8a8..416c9a45 100644
--- a/modules/local/spectrum2features/main.nf
+++ b/modules/local/spectrum2features/main.nf
@@ -2,10 +2,10 @@ process SPECTRUM2FEATURES {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(ms_file)

From df037e28253fe22b47b05a3e3f6d4934a1478025 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 22 Nov 2024 15:49:05 +0000
Subject: [PATCH 22/24] quantms-utils 0.0.13 -> 0.0.14

---
 modules/local/add_sage_feat/main.nf      | 6 +++---
 modules/local/diannconvert/main.nf       | 6 +++---
 modules/local/extract_psm/main.nf        | 6 +++---
 modules/local/extract_sample/main.nf     | 6 +++---
 modules/local/generate_diann_cfg/main.nf | 6 +++---
 modules/local/ms2rescore/main.nf         | 6 +++---
 modules/local/mzmlstatistics/main.nf     | 6 +++---
 modules/local/preprocess_expdesign.nf    | 6 +++---
 modules/local/samplesheet_check.nf       | 6 +++---
 modules/local/sdrfparsing/main.nf        | 6 +++---
 modules/local/spectrum2features/main.nf  | 6 +++---
 11 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf
index 052cc0b5..251b35e2 100644
--- a/modules/local/add_sage_feat/main.nf
+++ b/modules/local/add_sage_feat/main.nf
@@ -2,10 +2,10 @@ process SAGEFEATURE {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(extra_feat)
diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf
index 9608b918..b8680131 100644
--- a/modules/local/diannconvert/main.nf
+++ b/modules/local/diannconvert/main.nf
@@ -2,10 +2,10 @@ process DIANNCONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     path(report)
diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf
index e6c884b9..28c79935 100644
--- a/modules/local/extract_psm/main.nf
+++ b/modules/local/extract_psm/main.nf
@@ -2,10 +2,10 @@ process PSMCONVERSION {
     tag "$meta.mzml_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf
index f14e7693..c713258e 100644
--- a/modules/local/extract_sample/main.nf
+++ b/modules/local/extract_sample/main.nf
@@ -2,10 +2,10 @@ process GETSAMPLE {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf
index afd6123e..9947403c 100644
--- a/modules/local/generate_diann_cfg/main.nf
+++ b/modules/local/generate_diann_cfg/main.nf
@@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG {
     tag "$meta.experiment_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     val(meta)
diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf
index 228d7529..4e4ca40d 100644
--- a/modules/local/ms2rescore/main.nf
+++ b/modules/local/ms2rescore/main.nf
@@ -2,10 +2,10 @@ process MS2RESCORE {
     tag "$meta.mzml_id"
     label 'process_high'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     // userEmulation settings when docker is specified
     containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf
index 5ecb0958..5b0165a9 100644
--- a/modules/local/mzmlstatistics/main.nf
+++ b/modules/local/mzmlstatistics/main.nf
@@ -3,10 +3,10 @@ process MZMLSTATISTICS {
     label 'process_very_low'
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ms_file)
diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
index e9d66cf8..52d9d701 100644
--- a/modules/local/preprocess_expdesign.nf
+++ b/modules/local/preprocess_expdesign.nf
@@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     path design
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 6839b550..757e6717 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
     tag "$input_file"
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     path input_file
diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
index 8a26586b..aa71f71f 100644
--- a/modules/local/sdrfparsing/main.nf
+++ b/modules/local/sdrfparsing/main.nf
@@ -2,10 +2,10 @@ process SDRFPARSING {
     tag "$sdrf.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     path sdrf
diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf
index 416c9a45..c74ca498 100644
--- a/modules/local/spectrum2features/main.nf
+++ b/modules/local/spectrum2features/main.nf
@@ -2,10 +2,10 @@ process SPECTRUM2FEATURES {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.13"
+    conda "bioconda::quantms-utils=0.0.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.13--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.13--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.14--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.14--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(ms_file)

From effa1ba8581adb7099313cf08d1305aa5cc2fa58 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Thu, 21 Nov 2024 09:02:24 +0000
Subject: [PATCH 23/24] quantms-utils 0.0.12 -> 0.0.15

---
 modules/local/add_sage_feat/main.nf      | 6 +++---
 modules/local/diannconvert/main.nf       | 6 +++---
 modules/local/extract_psm/main.nf        | 6 +++---
 modules/local/extract_sample/main.nf     | 6 +++---
 modules/local/generate_diann_cfg/main.nf | 6 +++---
 modules/local/ms2rescore/main.nf         | 6 +++---
 modules/local/mzmlstatistics/main.nf     | 6 +++---
 modules/local/preprocess_expdesign.nf    | 6 +++---
 modules/local/samplesheet_check.nf       | 6 +++---
 modules/local/sdrfparsing/main.nf        | 6 +++---
 modules/local/spectrum2features/main.nf  | 6 +++---
 11 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/modules/local/add_sage_feat/main.nf b/modules/local/add_sage_feat/main.nf
index 395807d4..6acef0c4 100644
--- a/modules/local/add_sage_feat/main.nf
+++ b/modules/local/add_sage_feat/main.nf
@@ -2,10 +2,10 @@ process SAGEFEATURE {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(extra_feat)
diff --git a/modules/local/diannconvert/main.nf b/modules/local/diannconvert/main.nf
index 9e2f9e8b..e8bdfd99 100644
--- a/modules/local/diannconvert/main.nf
+++ b/modules/local/diannconvert/main.nf
@@ -2,10 +2,10 @@ process DIANNCONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     path(report)
diff --git a/modules/local/extract_psm/main.nf b/modules/local/extract_psm/main.nf
index af69fc82..58899a54 100644
--- a/modules/local/extract_psm/main.nf
+++ b/modules/local/extract_psm/main.nf
@@ -2,10 +2,10 @@ process PSMCONVERSION {
     tag "$meta.mzml_id"
     label 'process_medium'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf
index 359b88dc..3a67e9e1 100644
--- a/modules/local/extract_sample/main.nf
+++ b/modules/local/extract_sample/main.nf
@@ -2,10 +2,10 @@ process GETSAMPLE {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf
index 4a66bf8a..768db3ae 100644
--- a/modules/local/generate_diann_cfg/main.nf
+++ b/modules/local/generate_diann_cfg/main.nf
@@ -2,10 +2,10 @@ process GENERATE_DIANN_CFG {
     tag "$meta.experiment_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     val(meta)
diff --git a/modules/local/ms2rescore/main.nf b/modules/local/ms2rescore/main.nf
index 91a19f3e..e02a743f 100644
--- a/modules/local/ms2rescore/main.nf
+++ b/modules/local/ms2rescore/main.nf
@@ -2,10 +2,10 @@ process MS2RESCORE {
     tag "$meta.mzml_id"
     label 'process_high'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     // userEmulation settings when docker is specified
     containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
diff --git a/modules/local/mzmlstatistics/main.nf b/modules/local/mzmlstatistics/main.nf
index 51685bff..29918840 100644
--- a/modules/local/mzmlstatistics/main.nf
+++ b/modules/local/mzmlstatistics/main.nf
@@ -3,10 +3,10 @@ process MZMLSTATISTICS {
     label 'process_very_low'
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ms_file)
diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
index ceb79362..02937cb8 100644
--- a/modules/local/preprocess_expdesign.nf
+++ b/modules/local/preprocess_expdesign.nf
@@ -6,10 +6,10 @@ process PREPROCESS_EXPDESIGN {
     tag "$design.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     path design
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index 0749ef1c..f7c46fbc 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
     tag "$input_file"
     label 'process_single'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     path input_file
diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
index 2ac0427e..393c11e0 100644
--- a/modules/local/sdrfparsing/main.nf
+++ b/modules/local/sdrfparsing/main.nf
@@ -2,10 +2,10 @@ process SDRFPARSING {
     tag "$sdrf.Name"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     path sdrf
diff --git a/modules/local/spectrum2features/main.nf b/modules/local/spectrum2features/main.nf
index 9edce8a8..27cbb4ee 100644
--- a/modules/local/spectrum2features/main.nf
+++ b/modules/local/spectrum2features/main.nf
@@ -2,10 +2,10 @@ process SPECTRUM2FEATURES {
     tag "$meta.mzml_id"
     label 'process_low'
 
-    conda "bioconda::quantms-utils=0.0.12"
+    conda "bioconda::quantms-utils=0.0.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.12--pyhdfd78af_0' :
-        'biocontainers/quantms-utils:0.0.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/quantms-utils:0.0.15--pyhdfd78af_0' :
+        'biocontainers/quantms-utils:0.0.15--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(id_file), path(ms_file)

From c663c2fd1a01cc5745b6ef45e7cbfe47da9b3522 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Sat, 23 Nov 2024 17:32:55 +0000
Subject: [PATCH 24/24] quantms-utils 0.0.14 -> 0.0.15

---
 conf/pride_codon_slurm.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/pride_codon_slurm.config b/conf/pride_codon_slurm.config
index a9b4d7d9..c175f684 100644
--- a/conf/pride_codon_slurm.config
+++ b/conf/pride_codon_slurm.config
@@ -42,7 +42,7 @@ process {
     }
 
     withLabel: diann {
-        container = 'https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/tools/ghcr.io-bigbio-diann-1.9.1dev.sif'
+        container = '/hps/nobackup/juan/pride/reanalysis/singularity/ghcr.io-bigbio-diann-1.9.2.sif'
     }
 }