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' }"