Wrap-up patch release v3.3.1 (#113)

* Add pre-formatted database (#82)

* add pre-formatted database info

* add information about pre-formatted database

* 50 add tool integron finder 20 (#87)

* update version

* Add pre-formatted database (#83)

* add pre-formatted database info

* add information about pre-formatted database

* update falmeida-py package

* change version

* change main tools to public containers

* use biocontainer

* aggregate other non-biocontainer tools and diminish the size of docker images

* update module labels

* re-arranged docker images

* add integron_finder module

* update amrfinder version

* trying to addintegron finder to gff

* update docker

* fixed image install

* fixed integron finder 2 gff

* remove unnecessary grouptuple

* fix image and emboss module

* fix organization

* add docker image to module

* fix indentation

* fix indentation

* added integron finder results to final GFF and JBROWSE

* integron finder results added to HTML report

* fix docker image

* properly added to json summary

* update changelog

* update readme

* update list of tools

* update default config in docs

* backscape tildes

* update installation docs

* fix indentation

* update outputs docs

* fix wrong pipeline name

* fix typo

* update quickstart

* fixed mlst execution in singularity

* fix indentation

* 85 prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space (#89)

* add awk command to clean big fasta headers

* add awk statement to clean big fasta headers

* update bakta version

* fix bakta stats parsing

* 81 add tool mob suite (#90)

* Add pre-formatted database (#83)

* add pre-formatted database info

* add information about pre-formatted database

* add mob suite module

* added results to HTML report

* Update Dockerfile

* added mob_suite to json summary

* add tool to markdown files

* add tool information to docs

* add example reports

* update singularity config

* fixed kofamscan download

* fix dockerfile

* Fix unicycler tag

* use only docker images to avoid timeout error

* use docker ocntainer to avoid singularity timeout

* fixed resfinder for singularity

* fixed docker image

* fix gff2sql in singularity

* use proper singularity images

* fix singularity image download

* fixed docker image

* Add option for prebuilt db download (#94)

* include module to download pre-built databases

* update docs

* 69 tools to use own docker image (#91)

* moved container configurations of assembly modules

* update default flye version

* update container configuration for database-setup modules

* re-organize container definition of 'generic' modules

* reorganize container configuration for KO modules

* reorganized container configuration for MGEs modules

* finalizing container configuration reorganization of last modules

* containers already defined in config files

* update params schema

* fixed zenodo download

* mob_suite singularity image not always suited for low connection servers

* add option to download container configs

* update unicycler version (0.5.0--py310h6cc9453_3)

* 96 error summary for bugfix release (#101)

Update falmeida-py version

* 98 include ices and prophage annotation in json summary (#106)

* Try Dockerfile fix

* Update Dockerfile

* Update Dockerfile

* Update CHANGELOG.md

* 100 update pipeline docker images from docker tags to docker shasum (#108)

* fix singularity run options

* fix misc dockerfile

* update renv docker image environment

* update docker images to use shasum

* Update CHANGELOG.md

* 107 duplicate reads to unique read names (#109)

* Add pre-formatted database (#83)

* add pre-formatted database info

* add information about pre-formatted database

* update docs and fix report links

* include information of newly known issues (#103)

* add parameter to enable deduplication of reads

* Update manual.md

* update changelog

* Update docs for v3.3 (#110)

* update cli help

* Update installation.md

* add indentation

* Update README.md

* Update README.md

* fix tracedir

* always show from copy

* Update quickstart.md

* Update manual.md

* update citation information

* add citation example

* Update CHANGELOG.md

* 111 error on summary step when missing annotationidtxt key (#112)

* update for dev-testing

* adapt to antismash lite as the normal installation is horrible

* change for dev image

* updated docker image with stable 1.2.4 release of falmeida-py package for bugfix

* update changelog

Author: fmalmeida

conf/docker.config

@@ -18,7 +18,7 @@ process {
     // Custom pipeline's containers with various tools for general purposes
     //
     withLabel: 'db_download|db_tools|misc' {
-      container = 'fmalmeida/bacannot@sha256:726e085f1bd71b47c2d8a38fd46d812aab7eb8978bab7bf3cde3aa2b7b3e0f2c'
+      container = 'fmalmeida/bacannot@sha256:0648797837cd8e11b6abd40745cafc0db81647953921ec54ce0ceef9ecef6450'
     }
 
     // container for R tools

conf/singularity.config

@@ -18,7 +18,7 @@ process {
     // Custom pipeline's containers with various tools for general purposes
     //
     withLabel: 'db_download|db_tools|misc' {
-      container = 'docker://fmalmeida/bacannot@sha256:726e085f1bd71b47c2d8a38fd46d812aab7eb8978bab7bf3cde3aa2b7b3e0f2c'
+      container = 'docker://fmalmeida/bacannot@sha256:0648797837cd8e11b6abd40745cafc0db81647953921ec54ce0ceef9ecef6450'
     }
 
     // container for R tools

docker/misc/Dockerfile

@@ -81,7 +81,7 @@ ENV PATH=/work/digIS:$PATH
 
 # Create env for antismash
 RUN mamba create -y -n antismash -c bioconda -c conda-forge \
-      'bioconda::antismash>=6' 'anaconda::flask' 'anaconda::jinja2' 'anaconda::markupsafe' nomkl && \
+      'bioconda::antismash-lite>=6' 'anaconda::flask' 'anaconda::jinja2' 'anaconda::markupsafe' nomkl && \
       rm -rf /opt/conda/envs/antismash/lib/*/site-packages/antismash/databases && \
 	mamba clean -afy
 

docs/installation.md

@@ -29,15 +29,15 @@ The images are defined like the following:
 ```bash
 ...
 withLabel: 'db_download|db_tools|misc' {
-    container = 'fmalmeida/bacannot@sha256:726e085f1bd71b47c2d8a38fd46d812aab7eb8978bab7bf3cde3aa2b7b3e0f2c'
+    container = 'fmalmeida/bacannot@sha256:0648797837cd8e11b6abd40745cafc0db81647953921ec54ce0ceef9ecef6450'
 }
 ...
 ```
 
 And could be downloaded like this:
 
 ```bash
-docker pull fmalmeida/bacannot@sha256:726e085f1bd71b47c2d8a38fd46d812aab7eb8978bab7bf3cde3aa2b7b3e0f2c
+docker pull fmalmeida/bacannot@sha256:0648797837cd8e11b6abd40745cafc0db81647953921ec54ce0ceef9ecef6450
 ```
 
 > You would need to do it for each image.

markdown/CHANGELOG.md

@@ -2,6 +2,10 @@
 
 The tracking for changes started in v2.1
 
+## v3.3.1 [29-October-2023]
+
+* [[#111](https://github.com/fmalmeida/bacannot/issues/111)] -- Updated `falmeida-py` package version to fix problem with missing key for Summary.
+
 ## v3.3 [01-October-2023]
 
 * [[#50](https://github.com/fmalmeida/bacannot/issues/50)] -- Add `Integron Finder` tool to the pipeline