fmalmeida/ngs-preprocess v2.7.1

Release notes

v2.7.1

• [#36] - Include nf-tests to the pipeline.
• [#40] - Fix a problem when downloading PACBIO data.
• Adjust short-reads workflow filter to allow analysis from SRA for platform key-values: illumina, bgiseq and dnbseq

A new docker image was not created.

fmalmeida/ngs-preprocess v2.7.0

Release notes

• [#34] - Included a new tool in the pipeline (porechop ABI). Removed tracedir parameter. Build new docker image.

A new docker was built thus a new issue release was made.

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.

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)

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)

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.

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.

fmalmeida/ngs-preprocess v2.4.2

Release notes

v2.4.2 -- [2022-Oct-17]

Cleanup change. Short reads output are are now written as "preprocessed_reads/short_reads" 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)

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:

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 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)

fmalmeida/ngs-preprocess v2.4

Release notes

This version addresses the changes discussed in issue #7.

It has three main changes:

1. 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:

{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