From 2c65958c65661d544fa1a7af7428c2c0900b9708 Mon Sep 17 00:00:00 2001
From: yueqixuan <yueqx@foxmail.com>
Date: Thu, 16 Jul 2026 13:04:20 +0800
Subject: [PATCH] Fix bug and bump pmultiqc version

---
 modules/local/openms/msgf/main.nf |  8 ++++++--
 modules/local/pmultiqc/main.nf    | 14 +++++++-------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/modules/local/openms/msgf/main.nf b/modules/local/openms/msgf/main.nf
index ff54b4c06..44b43aa77 100644
--- a/modules/local/openms/msgf/main.nf
+++ b/modules/local/openms/msgf/main.nf
@@ -18,9 +18,13 @@ process MSGF {
     script:
     // The OpenMS adapters need the actual jar file, not the executable/shell wrapper that (bio)conda creates
     msgf_jar = ''
-    if ((workflow.containerEngine || (task.executor == "awsbatch")) && (task.container.indexOf("biocontainers") > -1 || task.container.indexOf("depot.galaxyproject.org") > -1)) {
+    if ((workflow.containerEngine || (task.executor == "awsbatch")) && task.container.indexOf("bigbio") > -1) {
+        msgf_jar = "-executable /opt/OpenMS/thirdparty/MSGFPlus/MSGFPlus.jar"
+    }
+    else if ((workflow.containerEngine || (task.executor == "awsbatch")) && (task.container.indexOf("biocontainers") > -1 || task.container.indexOf("depot.galaxyproject.org") > -1)) {
         msgf_jar = "-executable \$(find /usr/local/share/msgf_plus-*/MSGFPlus.jar -maxdepth 0)"
-    } else if (System.getenv('CONDA_PREFIX')) {
+    }
+    else if (System.getenv('CONDA_PREFIX')) {
         msgf_jar = "-executable \$(find \$CONDA_PREFIX/share/msgf_plus-*/MSGFPlus.jar -maxdepth 0)"
     }
 
diff --git a/modules/local/pmultiqc/main.nf b/modules/local/pmultiqc/main.nf
index d63efc7a9..6afd213e0 100644
--- a/modules/local/pmultiqc/main.nf
+++ b/modules/local/pmultiqc/main.nf
@@ -2,8 +2,8 @@ process PMULTIQC {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pmultiqc:0.0.39--pyhdfd78af_0' :
-        'biocontainers/pmultiqc:0.0.39--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/pmultiqc:0.0.45--pyhdfd78af_0' :
+        'biocontainers/pmultiqc:0.0.45--pyhdfd78af_0' }"
 
     input:
     path 'results/*'
@@ -17,10 +17,10 @@ process PMULTIQC {
 
     script:
     def args = task.ext.args ?: ''
-    def disable_pmultiqc = (params.enable_pmultiqc) && (params.export_mztab) ? "--quantms_plugin" : ""
-    def disable_table_plots = (params.enable_pmultiqc) && (params.skip_table_plots) ? "--disable_table" : ""
-    def disable_idxml_index = (params.enable_pmultiqc) && (params.pmultiqc_idxml_skip) ? "--ignored_idxml" : ""
-    def contaminant_affix = params.contaminant_string ? "--contaminant_affix ${params.contaminant_string}" : ""
+    def disable_pmultiqc = (params.enable_pmultiqc) && (params.export_mztab) ? "--quantms-plugin" : ""
+    def disable_table_plots = (params.enable_pmultiqc) && (params.skip_table_plots) ? "--disable-table" : ""
+    def disable_idxml_index = (params.enable_pmultiqc) && (params.pmultiqc_idxml_skip) ? "--ignored-idxml" : ""
+    def contaminant_affix = params.contaminant_string ? "--contaminant-affix ${params.contaminant_string}" : ""
 
     """
     set -x
@@ -39,7 +39,7 @@ process PMULTIQC {
         ${disable_table_plots} \\
         ${disable_idxml_index} \\
         ${contaminant_affix} \\
-        --quantification_method $params.quantification_method \\
+        --quantification-method $params.quantification_method \\
         ./results \\
         -o .