bump AGAT version to 1.2.0

NBISweden · Jan 10, 2024 · 5a7da8d · 5a7da8d
1 parent da60314
commit 5a7da8d
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Showing 9 changed files with 36 additions and 36 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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} \\