From 5a7da8d1a6c6b6a878ab40693213cfde1b9d8358 Mon Sep 17 00:00:00 2001 From: MartinPippel Date: Wed, 10 Jan 2024 16:11:37 +0100 Subject: [PATCH] bump AGAT version to 1.2.0 --- modules/local/agat/extractsequences.nf | 8 ++++---- modules/local/agat/filterbyattribute.nf | 8 ++++---- modules/local/agat/filterbylocusdistance.nf | 8 ++++---- modules/local/agat/filterbymrnablastvalue.nf | 8 ++++---- modules/local/agat/filterincompletegenecodingmodels.nf | 8 ++++---- modules/local/agat/gff2zff.nf | 8 ++++---- modules/local/agat/keeplongestisoform.nf | 8 ++++---- modules/local/agat/managefunctionalannotation.nf | 8 ++++---- modules/local/agat/separatebyrecord.nf | 8 ++++---- 9 files changed, 36 insertions(+), 36 deletions(-) diff --git a/modules/local/agat/extractsequences.nf b/modules/local/agat/extractsequences.nf index c8e7f20..cac5108 100644 --- a/modules/local/agat/extractsequences.nf +++ b/modules/local/agat/extractsequences.nf @@ -3,10 +3,10 @@ process AGAT_EXTRACTSEQUENCES { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path (gff) @@ -22,7 +22,7 @@ process AGAT_EXTRACTSEQUENCES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${gff.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_extract_sequences.pl \\ $args \\ diff --git a/modules/local/agat/filterbyattribute.nf b/modules/local/agat/filterbyattribute.nf index 048f8b4..1f5a026 100644 --- a/modules/local/agat/filterbyattribute.nf +++ b/modules/local/agat/filterbyattribute.nf @@ -3,10 +3,10 @@ process AGAT_FILTERBYATTRIBUTE { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path(mrna_gff) @@ -21,7 +21,7 @@ process AGAT_FILTERBYATTRIBUTE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${mrna_gff.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_filter_feature_by_attribute_value.pl \\ --gff ${mrna_gff} \\ diff --git a/modules/local/agat/filterbylocusdistance.nf b/modules/local/agat/filterbylocusdistance.nf index 5ad01a4..b8bde43 100644 --- a/modules/local/agat/filterbylocusdistance.nf +++ b/modules/local/agat/filterbylocusdistance.nf @@ -3,10 +3,10 @@ process AGAT_FILTERBYLOCUSDISTANCE { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path (coding_gene_features_gff) @@ -21,7 +21,7 @@ process AGAT_FILTERBYLOCUSDISTANCE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${coding_gene_features_gff.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_filter_by_locus_distance.pl \\ $args \\ diff --git a/modules/local/agat/filterbymrnablastvalue.nf b/modules/local/agat/filterbymrnablastvalue.nf index 29a7e49..bd23292 100644 --- a/modules/local/agat/filterbymrnablastvalue.nf +++ b/modules/local/agat/filterbymrnablastvalue.nf @@ -3,10 +3,10 @@ process AGAT_FILTERBYMRNABLASTVALUE { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path(gff) @@ -22,7 +22,7 @@ process AGAT_FILTERBYMRNABLASTVALUE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${gff.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_filter_by_mrnaBlastValue.pl \\ --gff $gff \\ diff --git a/modules/local/agat/filterincompletegenecodingmodels.nf b/modules/local/agat/filterincompletegenecodingmodels.nf index a6fd1e5..0f519cb 100644 --- a/modules/local/agat/filterincompletegenecodingmodels.nf +++ b/modules/local/agat/filterincompletegenecodingmodels.nf @@ -3,10 +3,10 @@ process AGAT_FILTERINCOMPLETEGENECODINGMODELS { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path (coding_gene_features_gff) @@ -22,7 +22,7 @@ process AGAT_FILTERINCOMPLETEGENECODINGMODELS { script: // def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${coding_gene_features_gff.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_filter_incomplete_gene_coding_models.pl \\ --gff ${coding_gene_features_gff} \\ diff --git a/modules/local/agat/gff2zff.nf b/modules/local/agat/gff2zff.nf index a91682b..7fc3cb1 100644 --- a/modules/local/agat/gff2zff.nf +++ b/modules/local/agat/gff2zff.nf @@ -2,10 +2,10 @@ process AGAT_GFF2ZFF { tag "${annotation}" label 'process_single' - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path (annotation) @@ -21,7 +21,7 @@ process AGAT_GFF2ZFF { script: // def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${genome.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_convert_sp_gff2zff.pl \\ --gff $annotation \\ diff --git a/modules/local/agat/keeplongestisoform.nf b/modules/local/agat/keeplongestisoform.nf index eecacb7..4e7f91f 100644 --- a/modules/local/agat/keeplongestisoform.nf +++ b/modules/local/agat/keeplongestisoform.nf @@ -3,10 +3,10 @@ process AGAT_KEEPLONGESTISOFORM { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path(coding_gene_features_gff) @@ -21,7 +21,7 @@ process AGAT_KEEPLONGESTISOFORM { script: // def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${coding_gene_features_gff.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_keep_longest_isoform.pl \\ -f ${coding_gene_features_gff} \\ diff --git a/modules/local/agat/managefunctionalannotation.nf b/modules/local/agat/managefunctionalannotation.nf index e35b728..4e3c0f6 100644 --- a/modules/local/agat/managefunctionalannotation.nf +++ b/modules/local/agat/managefunctionalannotation.nf @@ -3,10 +3,10 @@ process AGAT_MANAGEFUNCTIONALANNOTATION { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path(gff) @@ -25,7 +25,7 @@ process AGAT_MANAGEFUNCTIONALANNOTATION { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${gff.baseName}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_manage_functional_annotation.pl \\ $args \\ diff --git a/modules/local/agat/separatebyrecord.nf b/modules/local/agat/separatebyrecord.nf index 7c14356..c935213 100644 --- a/modules/local/agat/separatebyrecord.nf +++ b/modules/local/agat/separatebyrecord.nf @@ -3,10 +3,10 @@ process AGAT_SEPARATEBYRECORD { label 'process_single' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::agat=0.9.2" + conda "bioconda::agat=1.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/agat:0.9.2--pl5321hdfd78af_1': - 'biocontainers/agat:0.9.2--pl5321hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0': + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" input: tuple val(meta), path (gff) @@ -22,7 +22,7 @@ process AGAT_SEPARATEBYRECORD { script: // def args = task.ext.args ?: '' // def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '0.9.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '1.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ agat_sp_separate_by_record_type.pl \\ -g ${gff} \\