diff --git a/CHANGELOG.md b/CHANGELOG.md index 91d36e0e..a2f9f389 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). -## [3.2.1dev] - +## [3.3.0dev] - ### `Added` @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. | Dependency | Old version | New version | | ---------- | ----------- | ----------- | | multiqc | 1.14 | 1.18 | +| enchantr | 0.9.0 | 0.10.0 | ## [3.2.0] - 2023-10-27 Expecto patronum diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf index a1f67adf..fafbd052 100644 --- a/modules/local/airrflow_report/airrflow_report.nf +++ b/modules/local/airrflow_report/airrflow_report.nf @@ -6,8 +6,8 @@ process AIRRFLOW_REPORT { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: tuple val(meta), path(tab) // sequence tsv table in AIRR format diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf index af640cf5..ebec7209 100644 --- a/modules/local/enchantr/collapse_duplicates.nf +++ b/modules/local/enchantr/collapse_duplicates.nf @@ -8,8 +8,8 @@ process COLLAPSE_DUPLICATES { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ] diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf index e24c75d9..71deebc2 100644 --- a/modules/local/enchantr/define_clones.nf +++ b/modules/local/enchantr/define_clones.nf @@ -25,8 +25,8 @@ process DEFINE_CLONES { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf index 0267b81a..1ed10e8e 100644 --- a/modules/local/enchantr/detect_contamination.nf +++ b/modules/local/enchantr/detect_contamination.nf @@ -9,8 +9,8 @@ process DETECT_CONTAMINATION { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: path(tabs) diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf index b9a8de8e..e50a9e07 100644 --- a/modules/local/enchantr/dowser_lineages.nf +++ b/modules/local/enchantr/dowser_lineages.nf @@ -25,8 +25,8 @@ process DOWSER_LINEAGES { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: tuple val(meta), path(tabs) diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf index 08178111..89b1c3b8 100644 --- a/modules/local/enchantr/find_threshold.nf +++ b/modules/local/enchantr/find_threshold.nf @@ -25,8 +25,8 @@ process FIND_THRESHOLD { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf index 32522aa2..76f4e0b5 100644 --- a/modules/local/enchantr/remove_chimeric.nf +++ b/modules/local/enchantr/remove_chimeric.nf @@ -9,8 +9,8 @@ process REMOVE_CHIMERIC { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf index 804ebd61..ece9d93f 100644 --- a/modules/local/enchantr/report_file_size.nf +++ b/modules/local/enchantr/report_file_size.nf @@ -10,8 +10,8 @@ process REPORT_FILE_SIZE { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: path logs diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf index 36733e4d..6b232155 100644 --- a/modules/local/enchantr/single_cell_qc.nf +++ b/modules/local/enchantr/single_cell_qc.nf @@ -24,8 +24,8 @@ process SINGLE_CELL_QC { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: path(tabs) diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf index 224b391a..0dcd884e 100644 --- a/modules/local/enchantr/validate_input.nf +++ b/modules/local/enchantr/validate_input.nf @@ -10,8 +10,8 @@ process VALIDATE_INPUT { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: file samplesheet diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf index 0423695b..67c930d6 100644 --- a/modules/local/reveal/add_meta_to_tab.nf +++ b/modules/local/reveal/add_meta_to_tab.nf @@ -7,8 +7,8 @@ process ADD_META_TO_TAB { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" cache 'deep' // Without 'deep' this process would run when using -resume diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf index 75a06eac..c373ddbf 100644 --- a/modules/local/reveal/filter_junction_mod3.nf +++ b/modules/local/reveal/filter_junction_mod3.nf @@ -7,8 +7,8 @@ process FILTER_JUNCTION_MOD3 { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: tuple val(meta), path(tab) // sequence tsv in AIRR format diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf index abd71995..46062cb9 100644 --- a/modules/local/reveal/filter_quality.nf +++ b/modules/local/reveal/filter_quality.nf @@ -7,8 +7,8 @@ process FILTER_QUALITY { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/immcantation/airrflow:3.2.0': - 'docker.io/immcantation/airrflow:3.2.0' }" + 'docker.io/immcantation/airrflow:3.3.0': + 'docker.io/immcantation/airrflow:3.3.0' }" input: tuple val(meta), path(tab) // sequence tsv in AIRR format