bump to v2.1.1

rpetit3 · rpetit3 · commit 08d4bef99338 · 2022-07-10T00:30:00.000Z
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### `Added`
 - Add Panaroo to the `pangenome` Bactopia Tools
 - Add `genotyphi` and `seroba` to Merlin
+- bump `fastq-dl` to v1.1.1
 - Bactopia Tools (`bactopia --wf <NAME>`)
     - `busco` - Assembly completeness based on evolutionarily informed expectations
     - `genotyphi` - Salmonella Typhi genotyping with Mykrobe outputs
diff --git a/Dockerfile b/Dockerfile
@@ -2,7 +2,7 @@ FROM nfcore/base:2.1
 
 LABEL base.image="FROM nfcore/base:2.1"
 LABEL software="Bactopia"
-LABEL software.version="2.1.0"
+LABEL software.version="2.1.1"
 LABEL description="A flexible pipeline for complete analysis of bacterial genomes"
 LABEL website="https://bactopia.github.io/"
 LABEL license="https://github.com/bactopia/bactopia/blob/master/LICENSE"
diff --git a/bactopia/__init__.py b/bactopia/__init__.py
@@ -1,6 +1,6 @@
 """Top-level package for Bactopia."""
 
-__version__ = '2.1.0'
+__version__ = '2.1.1'
 
 __all__ = [
     'const',
diff --git a/bin/bactopia/bactopia b/bin/bactopia/bactopia
@@ -30,7 +30,7 @@
 # bactopia search --help
 # bactopia version
 # bactopia --help
-VERSION=2.1.0
+VERSION=2.1.1
 CONTAINER_VERSION="${VERSION%.*}.x"
 CONDA_ENV=$(which bactopia | sed 's=bin/bactopia==')
 BACTOPIA_NF="${CONDA_ENV}/share/bactopia-${CONTAINER_VERSION}" 
diff --git a/bin/bactopia/bactopia-citations.py b/bin/bactopia/bactopia-citations.py
@@ -12,7 +12,7 @@
 import os
 import sys
 
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 PROGRAM = "bactopia citations"
 DESCRIPTION = 'Prints the citations of datasets and tools used by Bactopia'
 
diff --git a/bin/bactopia/bactopia-datasets.py b/bin/bactopia/bactopia-datasets.py
@@ -9,7 +9,7 @@
 from executor import ExternalCommand, ExternalCommandFailed
 
 PROGRAM = "bactopia datasets"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 STDOUT = 11
 STDERR = 12
 CACHE_DIR = f'{os.path.expanduser("~")}/.bactopia'
diff --git a/bin/bactopia/bactopia-download.py b/bin/bactopia/bactopia-download.py
@@ -39,7 +39,7 @@
 import sys
 import time
 
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 PROGRAM = "bactopia download"
 STDOUT = 11
 STDERR = 12
diff --git a/bin/bactopia/bactopia-prepare.py b/bin/bactopia/bactopia-prepare.py
@@ -26,7 +26,7 @@
   --examples            Print examples of bactopia prepare and exit
   --version             show program's version number and exit
 """
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 PROGRAM = "bactopia prepare"
 import sys
 
diff --git a/bin/bactopia/bactopia-search.py b/bin/bactopia/bactopia-search.py
@@ -29,7 +29,7 @@
 """
 import os
 import sys
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 PROGRAM = "bactopia search"
 ENA_URL = ('https://www.ebi.ac.uk/ena/portal/api/search')
 FIELDS = [
diff --git a/bin/check-assembly-accession.py b/bin/check-assembly-accession.py
@@ -2,7 +2,7 @@
 """
 """
 PROGRAM = "check-assembly-accession"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 
 def check_assembly_version(accession):
diff --git a/bin/check-fastqs.py b/bin/check-fastqs.py
@@ -3,7 +3,7 @@
 Verifies input FASTQs meet minimum requirements.'
 """
 PROGRAM = "check-fastqs"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 
diff --git a/bin/cleanup-coverage.py b/bin/cleanup-coverage.py
@@ -12,7 +12,7 @@
   --version     show program's version number and exit
 """
 PROGRAM = "cleanup-coverage"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 def read_coverage(coverage):
diff --git a/bin/gh-actions/generate-nextflow-schema.py b/bin/gh-actions/generate-nextflow-schema.py
@@ -4,7 +4,7 @@
 """
 
 PROGRAM = "generate-nextflow-schema.py"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 REPO = "bactopia"
 
 BACTOPIA_SCHEMA = "conf/schema/bactopia.json"
diff --git a/bin/gh-actions/setup-docker-builds.py b/bin/gh-actions/setup-docker-builds.py
@@ -30,7 +30,7 @@
 from executor import ExternalCommand, ExternalCommandFailed
 
 PROGRAM = "setup-docker-builds.py"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 REPO = "bactopia"
 MAX_RETRY = 5
 STDOUT = 11
diff --git a/bin/helpers/create-subworkflow.sh b/bin/helpers/create-subworkflow.sh
@@ -2,7 +2,7 @@
 # build-containers
 #
 # Create a blank tool.
-VERSION=2.1.0
+VERSION=2.1.1
 
 if [[ $# == 0 ]]; then
     echo ""
diff --git a/bin/mask-consensus.py b/bin/mask-consensus.py
@@ -18,7 +18,7 @@
   --version     show program's version number and exit
 """
 PROGRAM = "mask-consensus"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 
diff --git a/bin/mlst-blast.py b/bin/mlst-blast.py
@@ -17,7 +17,7 @@
   --compressed  Input FASTA is Gzipped.
 """
 PROGRAM = "mlst-blast"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 def pipe_command(cmd_1, cmd_2, stdout=False, stderr=False, verbose=True,
                  shell=False):
diff --git a/bin/select-references.py b/bin/select-references.py
@@ -2,7 +2,7 @@
 """
 """
 PROGRAM = "select-references"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 
 def use_eutils(accession):
diff --git a/bin/split-coverages.py b/bin/split-coverages.py
@@ -2,7 +2,7 @@
 """
 """
 PROGRAM = "split-coverages"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 if __name__ == '__main__':
     import argparse as ap
diff --git a/conda/linux/annotate_genome.Dockerfile b/conda/linux/annotate_genome.Dockerfile
@@ -2,7 +2,7 @@ FROM nfcore/base:2.1
 
 LABEL base.image="nfcore/base:2.1"
 LABEL software="Bactopia - annotate_genome"
-LABEL software.version="2.1.0"
+LABEL software.version="2.1.1"
 LABEL description="A flexible pipeline for complete analysis of bacterial genomes"
 LABEL website="https://bactopia.github.io/"
 LABEL license="https://github.com/bactopia/bactopia/blob/master/LICENSE"
diff --git a/conda/linux/assemble_genome.Dockerfile b/conda/linux/assemble_genome.Dockerfile
@@ -2,7 +2,7 @@ FROM nfcore/base:2.1
 
 LABEL base.image="nfcore/base:2.1"
 LABEL software="Bactopia - assemble_genome"
-LABEL software.version="2.1.0"
+LABEL software.version="2.1.1"
 LABEL description="A flexible pipeline for complete analysis of bacterial genomes"
 LABEL website="https://bactopia.github.io/"
 LABEL license="https://github.com/bactopia/bactopia/blob/master/LICENSE"
diff --git a/conda/linux/assembly_qc.Dockerfile b/conda/linux/assembly_qc.Dockerfile
@@ -2,7 +2,7 @@ FROM nfcore/base:2.1
 
 LABEL base.image="nfcore/base:2.1"
 LABEL software="Bactopia - assembly_qc"
-LABEL software.version="2.1.0"
+LABEL software.version="2.1.1"
 LABEL description="A flexible pipeline for complete analysis of bacterial genomes"
 LABEL website="https://bactopia.github.io/"
 LABEL license="https://github.com/bactopia/bactopia/blob/master/LICENSE"
diff --git a/conda/linux/call_variants.Dockerfile b/conda/linux/call_variants.Dockerfile
@@ -2,7 +2,7 @@ FROM nfcore/base:2.1
 
 LABEL base.image="nfcore/base:2.1"
 LABEL software="Bactopia - call_variants"
-LABEL software.version="2.1.0"
+LABEL software.version="2.1.1"
 LABEL description="A flexible pipeline for complete analysis of bacterial genomes"
 LABEL website="https://bactopia.github.io/"
 LABEL license="https://github.com/bactopia/bactopia/blob/master/LICENSE"
diff --git a/conda/linux/gather_samples.Dockerfile b/conda/linux/gather_samples.Dockerfile
@@ -2,7 +2,7 @@ FROM nfcore/base:2.1
 
 LABEL base.image="nfcore/base:2.1"
 LABEL software="Bactopia - gather_samples"
-LABEL software.version="2.1.0"
+LABEL software.version="2.1.1"
 LABEL description="A flexible pipeline for complete analysis of bacterial genomes"
 LABEL website="https://bactopia.github.io/"
 LABEL license="https://github.com/bactopia/bactopia/blob/master/LICENSE"
diff --git a/conda/linux/minmers.Dockerfile b/conda/linux/minmers.Dockerfile
@@ -2,7 +2,7 @@ FROM nfcore/base:2.1
 
 LABEL base.image="nfcore/base:2.1"
 LABEL software="Bactopia - minmers"
-LABEL software.version="2.1.0"
+LABEL software.version="2.1.1"
 LABEL description="A flexible pipeline for complete analysis of bacterial genomes"
 LABEL website="https://bactopia.github.io/"
 LABEL license="https://github.com/bactopia/bactopia/blob/master/LICENSE"
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '2.1.0' %}
+{% set version = '2.1.1' %}
 
 package:
   name: bactopia
diff --git a/modules/local/bactopia/call_variants/bin/cleanup-coverage.py b/modules/local/bactopia/call_variants/bin/cleanup-coverage.py
@@ -12,7 +12,7 @@
   --version     show program's version number and exit
 """
 PROGRAM = "cleanup-coverage"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 def read_coverage(coverage):
diff --git a/modules/local/bactopia/call_variants/bin/mask-consensus.py b/modules/local/bactopia/call_variants/bin/mask-consensus.py
@@ -18,7 +18,7 @@
   --version     show program's version number and exit
 """
 PROGRAM = "mask-consensus"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 
diff --git a/modules/local/bactopia/call_variants/bin/select-references.py b/modules/local/bactopia/call_variants/bin/select-references.py
@@ -2,7 +2,7 @@
 """
 """
 PROGRAM = "select-references"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 
 def use_eutils(accession):
diff --git a/modules/local/bactopia/gather_samples/bin/check-assembly-accession.py b/modules/local/bactopia/gather_samples/bin/check-assembly-accession.py
@@ -2,7 +2,7 @@
 """
 """
 PROGRAM = "check-assembly-accession"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 
 def check_assembly_version(accession):
diff --git a/modules/local/bactopia/gather_samples/bin/check-fastqs.py b/modules/local/bactopia/gather_samples/bin/check-fastqs.py
@@ -3,7 +3,7 @@
 Verifies input FASTQs meet minimum requirements.'
 """
 PROGRAM = "check-fastqs"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 
diff --git a/modules/local/bactopia/mapping_query/bin/split-coverages.py b/modules/local/bactopia/mapping_query/bin/split-coverages.py
@@ -2,7 +2,7 @@
 """
 """
 PROGRAM = "split-coverages"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 if __name__ == '__main__':
     import argparse as ap
diff --git a/modules/local/bactopia/qc_reads/bin/check-fastqs.py b/modules/local/bactopia/qc_reads/bin/check-fastqs.py
@@ -3,7 +3,7 @@
 Verifies input FASTQs meet minimum requirements.'
 """
 PROGRAM = "check-fastqs"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 
diff --git a/modules/local/bactopia/sequence_type/bin/mlst-blast.py b/modules/local/bactopia/sequence_type/bin/mlst-blast.py
@@ -17,7 +17,7 @@
   --compressed  Input FASTA is Gzipped.
 """
 PROGRAM = "mlst-blast"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 
 def pipe_command(cmd_1, cmd_2, stdout=False, stderr=False, verbose=True,
                  shell=False):
diff --git a/modules/nf-core/modules/snippy/run/bin/cleanup-coverage.py b/modules/nf-core/modules/snippy/run/bin/cleanup-coverage.py
@@ -12,7 +12,7 @@
   --version     show program's version number and exit
 """
 PROGRAM = "cleanup-coverage"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 def read_coverage(coverage):
diff --git a/modules/nf-core/modules/snippy/run/bin/mask-consensus.py b/modules/nf-core/modules/snippy/run/bin/mask-consensus.py
@@ -18,7 +18,7 @@
   --version     show program's version number and exit
 """
 PROGRAM = "mask-consensus"
-VERSION = "2.1.0"
+VERSION = "2.1.1"
 import sys
 
 
diff --git a/nextflow.config b/nextflow.config
@@ -5,7 +5,7 @@ manifest {
     homePage = 'https://github.com/bactopia/bactopia'
     description = 'An extensive workflow for processing Illumina sequencing of bacterial genomes.'
     mainScript = 'main.nf'
-    version = '2.1.0'
+    version = '2.1.1'
     nextflowVersion = '>=19'
 }
 
