From f7d1bcb4d64c21f2bb4f25bab358416562f57d3c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 19 Sep 2024 10:19:38 +0200 Subject: [PATCH 1/3] Harshil align configs --- nextflow.config | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/nextflow.config b/nextflow.config index 9d4ff993..50295bc2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -314,20 +314,19 @@ profiles { executor.cpus = 4 executor.memory = 8.GB } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } - test_noprofiling { includeConfig 'conf/test_noprofiling.config' } - test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' } - test_nothing { includeConfig 'conf/test_nothing.config' } - test_motus { includeConfig 'conf/test_motus.config' } - test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' } - test_malt { includeConfig 'conf/test_malt.config' } - test_falco { includeConfig 'conf/test_falco.config' } - test_fastp { includeConfig 'conf/test_fastp.config' } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } + test_noprofiling { includeConfig 'conf/test_noprofiling.config' } + test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' } + test_nothing { includeConfig 'conf/test_nothing.config' } + test_motus { includeConfig 'conf/test_motus.config' } + test_krakenuniq { includeConfig 'conf/test_krakenuniq.config' } + test_malt { includeConfig 'conf/test_malt.config' } + test_falco { includeConfig 'conf/test_falco.config' } + test_fastp { includeConfig 'conf/test_fastp.config' } test_alternativepreprocessing { includeConfig 'conf/test_alternativepreprocessing.config' } - test_bbduk { includeConfig 'conf/test_bbduk.config' } - test_prinseqplusplus { includeConfig 'conf/test_prinseqplusplus.config' } - + test_bbduk { includeConfig 'conf/test_bbduk.config' } + test_prinseqplusplus { includeConfig 'conf/test_prinseqplusplus.config' } } // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile From 31554384ed6418d91ddd0b5b7e6c2818b585d990 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 19 Sep 2024 10:21:17 +0200 Subject: [PATCH 2/3] Unnecesary line --- subworkflows/local/longread_preprocessing.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf index 3b25879d..8b1590dc 100644 --- a/subworkflows/local/longread_preprocessing.nf +++ b/subworkflows/local/longread_preprocessing.nf @@ -39,7 +39,6 @@ workflow LONGREAD_PREPROCESSING { FASTQC_PROCESSED ( ch_processed_reads ) ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions ) ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip ) - } else if (params.preprocessing_qc_tool == 'falco') { FALCO_PROCESSED ( ch_processed_reads ) ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions ) From e6a44cf1898450def08bd923aaa24ed6f1420309 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 19 Sep 2024 10:22:53 +0200 Subject: [PATCH 3/3] Fix grammar --- subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf b/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf index 9a224154..9b4f6df5 100644 --- a/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf @@ -211,7 +211,7 @@ def toolCitationText() { "Long read preprocessing was performed with:", params.longread_adapterremoval_tool == "porechop_abi" ? "Porechop_ABI (Bonenfant et al. 2023)," : "", params.longread_adapterremoval_tool == "porechop" ? "Porechop (Wick et al. 2017)," : "", - params.longread_filter_tool == "filtlong" ? "Filtlong (Wick 2021)," : "", + params.longread_filter_tool == "filtlong" ? "Filtlong (Wick 2021)." : "", params.longread_filter_tool == "nanoq" ? "Nanoq (Steinig and Coin 2022)." : "", ].join(' ').trim()