From 58dffc0c5d4d710950dc2fe43555f353ce919f0a Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 11 Oct 2022 12:36:48 +0200 Subject: [PATCH 1/6] Add KrakenUniq and Filtlong in documentation --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 11eb9a3..1537a6f 100644 --- a/README.md +++ b/README.md @@ -32,8 +32,8 @@ On release, automated continuous integration tests run the pipeline on a full-si 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Performs optional read pre-processing - - Adapter clipping and merging (short read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long read: [porechop](https://github.com/rrwick/Porechop)) - - Low complexity filtering ([bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus)) + - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop)) + - Low complexity filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)) - Host read removal ([BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/)) - Run merging 3. Performs taxonomic profiling using one or more of: @@ -44,7 +44,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) - [Kaiju](https://kaiju.binf.ku.dk/) - [mOTUs](https://motu-tool.org/) - - [MetaMaps](https://github.com/DiltheyLab/MetaMaps) + - [KrakenUniq](https://github.com/fbreitwieser/krakenuniq) 4. Perform optional post-processing with: - [bracken](https://ccb.jhu.edu/software/bracken/) 5. Standardises output tables From dea45c66c24bc1bed23c1a6ea964e8d78dacd921 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 11 Oct 2022 14:59:48 +0200 Subject: [PATCH 2/6] Add Krona description --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 1537a6f..9385b33 100644 --- a/README.md +++ b/README.md @@ -49,6 +49,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - [bracken](https://ccb.jhu.edu/software/bracken/) 5. Standardises output tables 6. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +7. Plotting Kraken2, Centrifuge, Kaiju and MALT results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html)) ## Quick Start From 2423c9d87cef7c4c7588f21abdc5d46a85c18e66 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 11 Oct 2022 15:02:01 +0200 Subject: [PATCH 3/6] Add headers --- docs/usage.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/usage.md b/docs/usage.md index 8b8b588..4f4c1ac 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -47,6 +47,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data, as well as long-read FASTA files may look something like the one below. This is for 6 samples, where `2612` has been sequenced twice. ```console +sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta 2611,ERR5766174,ILLUMINA,,,///fasta/ERX5474930_ERR5766174_1.fa.gz 2612,ERR5766176,ILLUMINA,///fastq/ERX5474932_ERR5766176_1.fastq.gz,///fastq/ERX5474932_ERR5766176_2.fastq.gz, 2612,ERR5766180,ILLUMINA,///fastq/ERX5474936_ERR5766180_1.fastq.gz,, From f24344c168f6d98a8f58c38631557f5b9885f0e7 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 11 Oct 2022 16:30:42 +0200 Subject: [PATCH 4/6] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9385b33..73dfe93 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ On release, automated continuous integration tests run the pipeline on a full-si 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Performs optional read pre-processing - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop)) - - Low complexity filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)) + - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)) - Host read removal ([BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/)) - Run merging 3. Performs taxonomic profiling using one or more of: From 35b7fc26f7ab0711c6fcebe45806d807ed6d8d1e Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 11 Oct 2022 17:01:08 +0200 Subject: [PATCH 5/6] [skip ci] --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 73dfe93..8d45ff8 100644 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Quick Start -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) +1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`). 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. From bd56bc0ed629e5ecb012cd39c98b0f5aa3663335 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Wed, 12 Oct 2022 11:10:53 +0200 Subject: [PATCH 6/6] Add minimap2 and update contributors --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8d45ff8..2bd45a9 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ On release, automated continuous integration tests run the pipeline on a full-si 2. Performs optional read pre-processing - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop)) - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)) - - Host read removal ([BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/)) + - Host read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2)) - Run merging 3. Performs taxonomic profiling using one or more of: - [Kraken2](https://ccb.jhu.edu/software/kraken2/) @@ -88,7 +88,7 @@ nf-core/taxprofiler was originally written by nf-core community. We thank the following people for their extensive assistance in the development of this pipeline: -[James A. Fellows Yates](https://github.com/jfy133), [Moritz Beber](https://github.com/Midnighter), [Lauri Mesilaakso](https://github.com/ljmesi), [Sofia Stamouli](https://github.com/sofsam), [Maxime Borry](https://github.com/maxibor). +[James A. Fellows Yates](https://github.com/jfy133), [Moritz Beber](https://github.com/Midnighter), [Lauri Mesilaakso](https://github.com/ljmesi), [Sofia Stamouli](https://github.com/sofsam), [Maxime Borry](https://github.com/maxibor),[Thomas A. Christensen II](https://github.com/MillironX), [Jianhong Ou](https://github.com/jianhong), [Rafal Stepien](https://github.com/rafalstepien), [Mahwash Jamy](https://github.com/mjamy). ## Contributions and Support