diff --git a/modules/local/extract_sample/main.nf b/modules/local/extract_sample/main.nf
index 9781ae26..b9f1707e 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::sdrf-pipelines=0.0.25"
+    conda "bioconda::sdrf-pipelines=0.0.28"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.25--pyhdfd78af_0' :
-        'biocontainers/sdrf-pipelines:0.0.25--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.28--pyhdfd78af_0' :
+        'biocontainers/sdrf-pipelines:0.0.28--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/generate_diann_cfg/main.nf b/modules/local/generate_diann_cfg/main.nf
index fcd337e8..043dacb9 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 'conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.22'
+    conda 'conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.28'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.22--pyhdfd78af_0' :
-        'biocontainers/sdrf-pipelines:0.0.22--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.28--pyhdfd78af_0' :
+        'biocontainers/sdrf-pipelines:0.0.28--pyhdfd78af_0' }"
 
 
     input:
diff --git a/modules/local/preprocess_expdesign.nf b/modules/local/preprocess_expdesign.nf
index f6902da0..81edb63c 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::sdrf-pipelines=0.0.27"
+    conda "bioconda::sdrf-pipelines=0.0.28"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.27--pyhdfd78af_0' :
-        'biocontainers/sdrf-pipelines:0.0.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.28--pyhdfd78af_0' :
+        'biocontainers/sdrf-pipelines:0.0.28--pyhdfd78af_0' }"
 
     input:
     path design
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index f6c7bc1b..a91781cf 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::sdrf-pipelines=0.0.27"
+    conda "bioconda::sdrf-pipelines=0.0.28"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.27--pyhdfd78af_0' :
-        'biocontainers/sdrf-pipelines:0.0.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.28--pyhdfd78af_0' :
+        'biocontainers/sdrf-pipelines:0.0.28--pyhdfd78af_0' }"
 
     input:
     path input_file
diff --git a/modules/local/sdrfparsing/main.nf b/modules/local/sdrfparsing/main.nf
index 2a425c11..7f33a3dc 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 "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.27"
+    conda "conda-forge::pandas_schema bioconda::sdrf-pipelines=0.0.28"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.27--pyhdfd78af_0' :
-        'biocontainers/sdrf-pipelines:0.0.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/sdrf-pipelines:0.0.28--pyhdfd78af_0' :
+        'biocontainers/sdrf-pipelines:0.0.28--pyhdfd78af_0' }"
 
     input:
     path sdrf