Recent Releases of ngs-preprocess
ngs-preprocess - fmalmeida/ngs-preprocess v2.7.1
Release notes
v2.7.1
A new docker image was not created.
- Nextflow
Published by fmalmeida about 2 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.7.0
Release notes
- [#34] - Included a new tool in the pipeline (
porechop ABI). Removedtracedirparameter. Build new docker image.
A new docker was built thus a new issue release was made.
- Nextflow
Published by fmalmeida about 2 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.6.3
Release changes
v2.6.3 -- [2024-Fev-23]
- [#32] - Add as output a template samplesheet that can be readily used as input for MpGAP to assemble each downloaded read on its own.
- Nextflow
Published by fmalmeida over 2 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.6.2
Release notes
v2.6.2 -- [2024-Jan-19]
- [#24] - Added documentation on generated outputs, as requested in paper review
- [#25] - Added documentation exemplifying use for non bacterial dataset, as requested in paper review
- Small fixes on SRA module to allow downloading bgiseq data, and avoid running on empty lines
- Updated Dockerfile to name the maximum of versions possible
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)
- Nextflow
Published by fmalmeida over 2 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.6.1
Release notes
v2.6.1 -- [2023-Oct-26]
- [#21] - Added/updated citation information
- Small fix on pacbio download from sra
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)
- Nextflow
Published by fmalmeida over 2 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.6
Release notes
v2.6 -- [2023-Apr-16]
Small bug fixes on SRA_FETCH download modules. Updated pipeline to understand Illumina / BGIseq sequences for short reads. Updated Docker image with named versions of tools whenever possible.
More tools have been added so the versioning and docker image have now changed to v2.6.
- Nextflow
Published by fmalmeida about 3 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.5
Release notes
v2.5 -- [2022-Oct-30]
Add possibility for users to automatically fetch fastq files from SRA NCBI database. For that, users just need to use the --sra_ids parameter, passing a file with a list of SRA RunIDs, one per line.
More tools have been added so the versioning and docker image have now changed to v2.5.
- Nextflow
Published by fmalmeida over 3 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.4.2
Release notes
v2.4.2 -- [2022-Oct-17]
Cleanup change. Short reads output are are now written as "preprocessedreads/shortreads" instead of "preprocessed/illumina" as sometimes other technology may be used.
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)
- Nextflow
Published by fmalmeida over 3 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.4.1
Release notes
v2.4.1 -- [2022-Feb-21]
This version addresses the changes discussed in issue #10. It has three main changes:
- 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.
- Re-organized config files to keep structure cleaner
- Changed the standar 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)
- Nextflow
Published by fmalmeida over 4 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.4
Release notes
This version addresses the changes discussed in issue #7.
It has three main changes:
- The directory of outputs have been reorganized and the output files extension have been standardized in order to make it easier and simpler to use this pipeline as the first step of many analyses. It must look like this now:
console
{OUTPUT}
├── final_output # the final preprocessed reads of any tech (organized in folders)
│ ├── illumina # final preprocessed illumina reads
│ │ ├── SRR8482585_30X.merged.fq.gz
│ │ ├── SRR8482585_30X_R1.unmerged.fq.gz
│ │ └── SRR8482585_30X_R2.unmerged.fq.gz
│ ├── nanopore # final preprocessed nanopore reads
│ │ └── kp_30X.filtered.fq.gz
│ └── pacbio # final preprocessed pacbio reads
│ └── lima.bc1018--bc1018.filtered.fq.gz
└── preprocessing_outputs # here will be saved (per tech) the files (QC, Logs, Stats) generated during preprocessing
├── illumina
│ ├── SRR8482585_30X_fastp.html
│ └── SRR8482585_30X_fastp.json
├── nanopore
│ ├── QC
│ │ ├── kp_30X_nanoQC
│ │ ├── kp_30X_nanoplot
│ │ └── kp_30X_stats
│ └── porechop
│ └── kp_30X.trimmed.fq.gz
└── pacbio
├── QC
│ ├── lima.bc1018--bc1018_nanoQC
│ ├── lima.bc1018--bc1018_nanoplot
│ └── lima.bc1018--bc1018_stats
└── bam2fastq
├── lima.bc1018--bc1018.bam.pbi
└── lima.bc1018--bc1018.fq.gz
2. Secondly, the pipelines tools/dependencies for preprocessing Illumina reads have changed. Now, instead of using flash, trim_galore, fastqc and lighter, the pipeline will use only fastp which performs all the steps that were done by these tools, but much faster since it is written in C++.
3. The parameter --outdir is now --output for better readability
- Nextflow
Published by fmalmeida over 4 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.3
The pipeline
ngs-preprocess is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. It is an easy to use pipeline that uses state-of-the-art software for quality check and pre-processing ngs reads of Illumina, Pacbio and Oxford Nanopore Technologies.
Version
Relase notes
In summary, this release reconfigures the pipeline to be more likely nf-core pipelines enabling users to run it with docker, singularity or conda. The release notes can be checked in the CHANGELOG.md.
- Nextflow
Published by fmalmeida over 4 years ago
ngs-preprocess - fmalmeida/ngs-preprocess v2.2
The pipeline
ngs-preprocess, is a customisable easy to use pipeline that uses state-of-the-art software for pre-procesing ngs reads of Illumina, Pacbio and Oxford Nanopore Technologies sequencing platforms having only Docker and Nextflow as dependencies.
Version
The latest changes applied from version 2.1 to 2.2 are described in the CHANGELOG.md file.
- Nextflow
Published by fmalmeida over 5 years ago
ngs-preprocess - fmalmeida/NGS-preprocess v2.1
Changes
Fixed problems with pacbio data
Now working with pacbio legacy data in *.bas.h5 format and in new *.bam format
- Nextflow
Published by fmalmeida about 6 years ago
ngs-preprocess - fmalmeida/NGS-preprocess v2.0
This version marks the change from Nextflow DSL 1 to Nextflow DSL 2.
This change will make it easier for users to customize the pipeline in their own way.
- Nextflow
Published by fmalmeida over 6 years ago