diff --git a/README.md b/README.md index 0b4c71e7..aa63b68d 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ ## Introduction -**plant-food-research-open/assemblyqc** is a [Nextflow](https://www.nextflow.io/docs/latest/index.html) pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report. The tools are shown in the [Pipeline Flowchart](#pipeline-flowchart) and their references are listed in [CITATIONS.md](./CITATIONS.md). The pipeline includes skip flags to disable execution of many of it tools. +**plant-food-research-open/assemblyqc** is a [Nextflow](https://www.nextflow.io/docs/latest/index.html) pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report. The tools are shown in the [Pipeline Flowchart](#pipeline-flowchart) and their references are listed in [CITATIONS.md](./CITATIONS.md). The pipeline includes skip flags to disable execution of various tools. ## Pipeline Flowchart @@ -29,7 +29,7 @@ - [Kraken 2](https://github.com/DerrickWood/kraken2), [Krona](https://github.com/marbl/Krona): Taxonomy classification - `Alignment and visualisation of HiC data` - [sra-tools](https://github.com/ncbi/sra-tools): HiC data download from SRA or use of local FASTQ files - - [fastp](https://github.com/OpenGene/fastp), [FastQC](https://github.com/s-andrews/FastQC): QC and trimming + - [fastp](https://github.com/OpenGene/fastp), [FastQC](https://github.com/s-andrews/FastQC): Read QC and trimming - [SeqKit sort](https://github.com/shenwei356/seqkit): Alphanumeric sorting of FASTA by sequence ID - [bwa-mem](https://github.com/lh3/bwa): HiC read alignment - [samblaster](https://github.com/GregoryFaust/samblaster): Duplicate marking @@ -43,7 +43,7 @@ - [Merqury](https://github.com/marbl/merqury): Completeness, consensus quality and phasing assessment - `Synteny analysis` - [MUMmer](https://github.com/mummer4/mummer) → [Circos](http://circos.ca/documentation/) + [dotplot](https://plotly.com): One-to-all and all-to-all synteny analysis at the contig level - - [Minimap2](https://github.com/lh3/minimap2) → [Syri](https://github.com/schneebergerlab/syri)/[Plotsr](https://github.com/schneebergerlab/plotsr): One-one to chromosome synteny analysis at the chromosome level + - [Minimap2](https://github.com/lh3/minimap2) → [Syri](https://github.com/schneebergerlab/syri)/[Plotsr](https://github.com/schneebergerlab/plotsr): One-to-one synteny analysis at the chromosome level - `Annotation` - [GenomeTools gt gff3validator](https://genometools.org/tools/gt_gff3validator.html) + [FASTA/GFF correspondence](subworkflows/gallvp/gff3_gt_gff3_gff3validator_stat/main.nf): GFF3 validation - [GenomeTools gt stat](https://genometools.org/tools/gt_stat.html): Annotation statistics diff --git a/tests/nextflow.config b/tests/nextflow.config index 1d5de542..ed1a8053 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -5,7 +5,7 @@ */ params { - modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' } timeline { enabled = false }