diff --git a/modules/local/ensure_fastq_extension.nf b/modules/local/ensure_fastq_extension.nf
index 6de223b..034c9bb 100644
--- a/modules/local/ensure_fastq_extension.nf
+++ b/modules/local/ensure_fastq_extension.nf
@@ -2,7 +2,7 @@ process ENSURE_FASTQ_EXTENSION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::bash=5.0" : null)
+    conda "conda-forge::bash=5.0
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
         'biocontainers/biocontainers:v1.2.0_cv2' }"
diff --git a/modules/local/kraken2_standard_report.nf b/modules/local/kraken2_standard_report.nf
index 09a98c1..4169c3a 100644
--- a/modules/local/kraken2_standard_report.nf
+++ b/modules/local/kraken2_standard_report.nf
@@ -2,7 +2,7 @@ process KRAKEN2_STANDARD_REPORT {
     tag "$meta.id"
     label 'process_single'
 
-    conda (params.enable_conda ? 'conda-forge::sed=4.8' : null)
+    conda "conda-forge::sed=4.8"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
         'biocontainers/biocontainers:v1.2.0_cv2' }"
diff --git a/modules/local/krona_cleanup.nf b/modules/local/krona_cleanup.nf
index 804cb69..f13dcc8 100644
--- a/modules/local/krona_cleanup.nf
+++ b/modules/local/krona_cleanup.nf
@@ -2,7 +2,7 @@ process KRONA_CLEANUP {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
         'biocontainers/biocontainers:v1.2.0_cv1' }"
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index d1693be..7a09573 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -29,7 +29,7 @@ if ( params.input ) {
 
 if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' }
 
-if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
+if (!params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
 if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
 
 if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' ))  exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"