fmalmeida/mpgap v3.2.2

Release Notes

v3.2.2 -- [2024-Sep-06]

• #82
  • Small fix to allow canu to use -pacbio-hifi parameter when using --high_quality_longreads pipeline parameter. For nanopore it stays using -corrected since canu does not have a special option for high-quality nanopore data.

fmalmeida/mpgap v3.2.1

Release notes

v3.2.1 -- [2024-Jul-24]

• #77
  • Add cleanup to avoid overwrite existing files error in BUSCO when resuming a run.
• #79
  • Add if-else in MultiQC module so that if Quast report has different set of columns.

fmalmeida/mpgap v3.2.0

Release notes

• Update unicyler to v0.5.0
• Adjust Pilon polishing module to select how many rounds of polishing to run. Default is 4.
• Adjust raven module to allow pre-set -k and -w values for corrected/high-quality longreads, while allowing user modification
• Increase default --max_memory value to 20.GB.
• Added to parameters to allow users to quickly update how many resources the first attempt of an assembly task should ask
  • --start_asm_cpus
  • --start_asm_mem
• Add a directory called final_assemblies in the main output directory holding all the assemblies generated in the pipeline execution.
• Updated documentation as discussed in [#58] and [#57].
• [#50]
  • Parameters --skip_pilon and --skip_polypolish added to the pipeline
  • MultiQC report was fixed and enhanced
  • Docker image was also modified to download BUSCO standalone and pipeline perform the BUSCO standalone run instead of via quast.
• [#53] - Include hifiasm assembler in the pipeline. Long reads only and hybrid strategy 2.
• [#61] - Add a simple parameter to adjust how many cpus and how much memory should the assembly jobs request in the first attempt to avoid lack of resources errors.
• [#66] - Include an automated generation of a samplesheet for bacannot pipeline.
• [#72] - hifiasm is only executed for corrected (or high quality) longreads

fmalmeida/MpGAP v3.1.4

Release notes

v3.1.4 -- [2022-Sep-03]

This version addresses the changes discussed in #36, #37 and #38.
Its main changes are:

• Solving the problem of loading a parameter that accepts either integer or string by removing check-up from JSON schema and creating a customized check-up.
• Added 'error_retry' label to haslr as sometimes it radomnly fails.
• added a .gitpod.yml
• Customized labels to ask for a little bit more on first run
• Added a module config for quast to ask for more memory and cpus on first run, removing it from 'process_low' label
• Added a simple command in pilon module to ensure it starts with a "fresh" output dir to place results
• Added a new option called --skip_raw_assemblies_polishing which, when running hybrid strategy 2 avoids polishing raw long reads assemblies with short reads, instead, it only polishes the assemblies that have been already polished with medaka.

fmalmeida/MpGAP v3.1.3

Release Notes

v3.1.3 -- [2022-Mar-03]

Although Megahit was already present inside the docker image and the core of the pipeline as it was used by Shovill, Shovill is an assembler focused in bacterias, and, in their manual, they instruct users to run Megahit directly when working with non-bacterial samples.

Thus, we've seen the need to incorporate a new module that runs Megahit directly as well instead of only underneath Shovill.

Nothing has changed in terms of how tools are called and used, thus the docker image still the same. In fact, patch/fix releases (x.x.x) will always use the docker from breaking/features release (x.x)

fmalmeida/MpGAP v3.1.2

Release notes

v3.1.2 -- [2022-Feb-28]

This version addresses the changes discussed in issue #33. It has three main changes:

1. Added standard NF allocation resource rules as it is done by nf-core community
   • It also uses templates of CLI help and logging messages from nf-core community.
2. Re-organized config files to keep structure cleaner
3. Changed the standard profile which will not load docker by default anymore. As it is the common practice for NF pipelines, user must explicitily select between docker/conda/singularity profiles.

Nothing has changed in terms of how tools are called and used, thus the docker image still the same. In fact, patch/fix releases (x.x.x) will always use the docker from breaking/features release (x.x)

fmalmeida/MpGAP v3.1.1

Release notes

This is a super small release that is basically a hotfix. It solved the following:

• updated the documentation since a few parameters used in the samplesheet were missing its explanation in the manual. Related to issue #29
• Updated the quast process to understand when it is being executed in docker/conda/singularity profiles. This was necessary because, for singularity, another line of code was required to prepare the busco images from the docker to be used, which was not required in docker and conda and would raise errors in these profiles.

fmalmeida/MpGAP v3.1

Release notes

This release addresses the issue #17.

Now the pipeline mainly relies on packages built through conda into a main environment, making it possible to use it with docker, conda or singularity by properly using the -profile parameter.

Please read more about it at: https://github.com/fmalmeida/MpGAP#selecting-between-profiles

Compatibility

Because a few tools do not have conda packages, or they are not up-to-date causing incompatibilities when producing the main conda environment ... Pre-compiled binaries for these tools have been made available inside the main/root pipeline bin directory. Therefore, the -profile conda will only work in linux-64 systems. Users in other operating systems must use docker or singularity.

fmalmeida/MpGAP v3.0.1

The pipeline

MpGAP, is a very customisable (easy to use) pipeline that uses state-of-the-art software for the de novo assembly of sequencing reads. It is capable of performing short reads only, long reads only and hybrid assemblies using data from Illumina, Pacbio and Oxford Nanopore Technologies sequencing platforms. As a plus, it has only Docker and Nextflow as dependencies.

Relase notes

Super small fix to properly load YAML file when using the pipeline with cloud computing environments such as AWS/S3-bucket:

# from
parameter_yaml = new FileInputStream(new File(params.input))
# to
parameter_yaml = file(params.input).readLines().join("\n")

fmalmeida/MpGAP v3.0

The pipeline

MpGAP, is a very customisable (easy to use) pipeline that uses state-of-the-art software for the de novo assembly of sequencing reads. It is capable of performing short reads only, long reads only and hybrid assemblies using data from Illumina, Pacbio and Oxford Nanopore Technologies sequencing platforms. As a plus, it has only Docker and Nextflow as dependencies.

Relase notes

In summary, this release reconfigures the pipeline to load input data from a samplesheet in order to make it possible to seamlessly analyse multiple samples at once. The release notes can be checked in the CHANGELOG.md.