From dc4067f7b4906d100f5104330707d9189321fd99 Mon Sep 17 00:00:00 2001 From: d4straub Date: Tue, 26 Mar 2024 13:28:50 +0100 Subject: [PATCH] update DADA2 --- modules/local/cutadapt_summary_merge.nf | 6 +++--- modules/local/dada2_addspecies.nf | 6 +++--- modules/local/dada2_denoising.nf | 6 +++--- modules/local/dada2_err.nf | 6 +++--- modules/local/dada2_filtntrim.nf | 6 +++--- modules/local/dada2_quality.nf | 6 +++--- modules/local/dada2_rmchimera.nf | 6 +++--- modules/local/dada2_stats.nf | 6 +++--- modules/local/dada2_taxonomy.nf | 6 +++--- modules/local/format_pplacetax.nf | 6 +++--- modules/local/merge_stats.nf | 6 +++--- modules/local/metadata_all.nf | 6 +++--- modules/local/metadata_pairwise.nf | 6 +++--- modules/local/novaseq_err.nf | 6 +++--- 14 files changed, 42 insertions(+), 42 deletions(-) diff --git a/modules/local/cutadapt_summary_merge.nf b/modules/local/cutadapt_summary_merge.nf index 2b25fb422..d3ce87582 100644 --- a/modules/local/cutadapt_summary_merge.nf +++ b/modules/local/cutadapt_summary_merge.nf @@ -2,10 +2,10 @@ process CUTADAPT_SUMMARY_MERGE { tag "${files}" label 'process_low' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: val(action) diff --git a/modules/local/dada2_addspecies.nf b/modules/local/dada2_addspecies.nf index 6f5282642..8976648fe 100644 --- a/modules/local/dada2_addspecies.nf +++ b/modules/local/dada2_addspecies.nf @@ -3,10 +3,10 @@ process DADA2_ADDSPECIES { label 'process_high' label 'single_cpu' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: path(taxtable) diff --git a/modules/local/dada2_denoising.nf b/modules/local/dada2_denoising.nf index 2cf7fa1bd..637bd8981 100644 --- a/modules/local/dada2_denoising.nf +++ b/modules/local/dada2_denoising.nf @@ -3,10 +3,10 @@ process DADA2_DENOISING { label 'process_medium' label 'process_long' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path("filtered/*"), path(errormodel) diff --git a/modules/local/dada2_err.nf b/modules/local/dada2_err.nf index 0c9357e96..9f463292b 100644 --- a/modules/local/dada2_err.nf +++ b/modules/local/dada2_err.nf @@ -2,10 +2,10 @@ process DADA2_ERR { tag "$meta.run" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/dada2_filtntrim.nf b/modules/local/dada2_filtntrim.nf index 9aca59129..a2a015c20 100644 --- a/modules/local/dada2_filtntrim.nf +++ b/modules/local/dada2_filtntrim.nf @@ -2,10 +2,10 @@ process DADA2_FILTNTRIM { tag "$meta.id" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path(reads), val(trunclenf), val(trunclenr) diff --git a/modules/local/dada2_quality.nf b/modules/local/dada2_quality.nf index ff91c9958..5401497a3 100644 --- a/modules/local/dada2_quality.nf +++ b/modules/local/dada2_quality.nf @@ -2,10 +2,10 @@ process DADA2_QUALITY { tag "$meta" label 'process_low' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/dada2_rmchimera.nf b/modules/local/dada2_rmchimera.nf index 4e14ce1cb..0ba546b73 100644 --- a/modules/local/dada2_rmchimera.nf +++ b/modules/local/dada2_rmchimera.nf @@ -2,10 +2,10 @@ process DADA2_RMCHIMERA { tag "$meta.run" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path(seqtab) diff --git a/modules/local/dada2_stats.nf b/modules/local/dada2_stats.nf index f4112046c..eb36195bc 100644 --- a/modules/local/dada2_stats.nf +++ b/modules/local/dada2_stats.nf @@ -2,10 +2,10 @@ process DADA2_STATS { tag "$meta.run" label 'process_low' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path("filter_and_trim_files/*"), path(denoised), path(mergers), path(seqtab_nochim) diff --git a/modules/local/dada2_taxonomy.nf b/modules/local/dada2_taxonomy.nf index 4be292d27..0a2c28f66 100644 --- a/modules/local/dada2_taxonomy.nf +++ b/modules/local/dada2_taxonomy.nf @@ -2,10 +2,10 @@ process DADA2_TAXONOMY { tag "${fasta},${database}" label 'process_high' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: path(fasta) diff --git a/modules/local/format_pplacetax.nf b/modules/local/format_pplacetax.nf index 1861a3657..92930b19d 100644 --- a/modules/local/format_pplacetax.nf +++ b/modules/local/format_pplacetax.nf @@ -2,10 +2,10 @@ process FORMAT_PPLACETAX { tag "${tax.baseName}" label 'process_high' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path(tax) diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf index b2e2cb8cb..d9343f5ac 100644 --- a/modules/local/merge_stats.nf +++ b/modules/local/merge_stats.nf @@ -1,10 +1,10 @@ process MERGE_STATS { label 'process_low' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: path('file1.tsv') diff --git a/modules/local/metadata_all.nf b/modules/local/metadata_all.nf index 8993d1ca3..770f994c7 100644 --- a/modules/local/metadata_all.nf +++ b/modules/local/metadata_all.nf @@ -2,10 +2,10 @@ process METADATA_ALL { tag "$metadata" label 'process_low' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: path(metadata) diff --git a/modules/local/metadata_pairwise.nf b/modules/local/metadata_pairwise.nf index 6dd9ab116..a4aa7e067 100644 --- a/modules/local/metadata_pairwise.nf +++ b/modules/local/metadata_pairwise.nf @@ -2,10 +2,10 @@ process METADATA_PAIRWISE { tag "$metadata" label 'process_low' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: path(metadata) diff --git a/modules/local/novaseq_err.nf b/modules/local/novaseq_err.nf index 991fa803c..30e113fd9 100644 --- a/modules/local/novaseq_err.nf +++ b/modules/local/novaseq_err.nf @@ -2,10 +2,10 @@ process NOVASEQ_ERR { tag "$meta.run" label 'process_medium' - conda "bioconda::bioconductor-dada2=1.28.0" + conda "bioconda::bioconductor-dada2=1.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' : - 'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' : + 'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }" input: tuple val(meta), path(errormodel)