From 2d646285524cd17b203a69680a198bfbf79b227f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 20 Jan 2023 13:33:43 +0100 Subject: [PATCH 1/2] Fix left-over warns from loca modules --- modules/local/ensure_fastq_extension.nf | 2 +- modules/local/kraken2_standard_report.nf | 2 +- modules/local/krona_cleanup.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) 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' }" From cac6f54d2d67b64e23e591813678f052afe20406 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 20 Jan 2023 13:36:17 +0100 Subject: [PATCH 2/2] [extra] Fix warn related to recently changed parameter --- workflows/taxprofiler.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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'"