Merge pull request #444 from ypriverol/dev

update container for msgf_plus indexing.
bigbio · Nov 25, 2024 · d5f3d5a · d5f3d5a
2 parents 0a8d513 + 6ff2db1
commit d5f3d5a
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diff --git a/conf/pride_codon_slurm.config b/conf/pride_codon_slurm.config
@@ -27,7 +27,7 @@ singularity {
 process {
     // this is to avoid errors for missing files due to shared filesystem latency
     maxRetries    = 30
-    errorStrategy = { task.exitStatus in ((130..145) + 104 + 1 + 9 + 134 + 97 + 137 + 0) ? "retry" : "terminate" }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 1 + 9 + 134 + 97 + 0) ? "retry" : "terminate" }
     cache         = "lenient"
     afterScript   = "sleep 60"
 

diff --git a/modules/local/openms/thirdparty/msgfdb_indexing/main.nf b/modules/local/openms/thirdparty/msgfdb_indexing/main.nf
@@ -3,10 +3,10 @@ process MSGFDBINDEXING {
     label 'process_low'
     label 'openms'
 
-    conda "bioconda::openms-thirdparty=3.2.0"
+    conda "bioconda::msgf_plus=2024.03.26"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.2.0--h9ee0642_4' :
-        'biocontainers/openms-thirdparty:3.2.0--h9ee0642_4' }"
+        'https://depot.galaxyproject.org/singularity/msgf_plus:2024.03.26--hdfd78af_0' :
+        'biocontainers/msgf_plus:2024.03.26--hdfd78af_0' }"
 
     input:
     path(database)