diff --git a/CHANGELOG.md b/CHANGELOG.md index 94639d49..4ab9c061 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- [#758](https://github.com/nf-core/mag/pull/758) - Added new diagram in metro-map style (by @jfy133, @prototaxites, @d4straub) + ### `Changed` - [#731](https://github.com/nf-core/mag/pull/747) - Updated to nf-core 3.1.2 `TEMPLATE` (by @jfy133) diff --git a/docs/images/mag_metromap_dark.png b/docs/images/mag_metromap_dark.png new file mode 100644 index 00000000..ec11e949 Binary files /dev/null and b/docs/images/mag_metromap_dark.png differ diff --git a/docs/images/mag_metromap_dark.svg b/docs/images/mag_metromap_dark.svg new file mode 100644 index 00000000..3d72ca77 --- /dev/null +++ b/docs/images/mag_metromap_dark.svg @@ -0,0 +1,2194 @@ + + + +DASToolShort readsLong readsAssembled sequencesGenome binsMultipleparalleloptionsSingle choiceDefaultOpt-in + + +nf-core/magv3.3STARTKraken2 /CentrifugeNanoplot(Raw)Nanolyse /chopperFiltlong /NanoqchopperNanoplot(Filtered)porechop /oporechop_ABIFastQC(Trimmed)FastQC(Raw)Bowtie2 (Host)Run merge Bowtie2(PhiX)BBNormKronafastp/AdapterRemovalMEGAHIT / SPAdes /SPAdes hybridProdigal /geNomadQUAST345fastqfastqfastqfastq12Bowtie2 (Contigs)pyDamageFreeBayesBCFToolsMetaBat2 /MaxBin2 /CONCOCT6TiaraGUNCPROKKAMetaEuk89GTDBTK / CATBUSCO / CheckM / CheckM2QUASTShort-read adapter/host/PhiX removal, normalisationLong-read adapter/host/Lambda removal, quality filteringContig binning7Bin refinementBin quality evaluationBin taxonomic classificationand annotationENDMultiQC/Bin Summary10Run summaryShort read taxonomic classificationDe novo assembly, contig evaluation & annotationAncient contig identificationand damage correction diff --git a/docs/images/mag_metromap_light.png b/docs/images/mag_metromap_light.png new file mode 100644 index 00000000..9f34ffa7 Binary files /dev/null and b/docs/images/mag_metromap_light.png differ diff --git a/docs/images/mag_metromap_light.svg b/docs/images/mag_metromap_light.svg new file mode 100644 index 00000000..35442f85 --- /dev/null +++ b/docs/images/mag_metromap_light.svg @@ -0,0 +1,2194 @@ + + + +DASToolShort readsLong readsAssembled sequencesGenome binsMultipleparalleloptionsSingle choiceDefaultOpt-in + + +nf-core/magv3.3STARTKraken2 /CentrifugeNanoplot(Raw)Nanolyse /chopperFiltlong /NanoqchopperNanoplot(Filtered)porechop /oporechop_ABIFastQC(Trimmed)FastQC(Raw)Bowtie2 (Host)Run merge Bowtie2(PhiX)BBNormKronafastp/AdapterRemovalMEGAHIT / SPAdes /SPAdes hybridProdigal /geNomadQUAST345fastqfastqfastqfastq12Bowtie2 (Contigs)pyDamageFreeBayesBCFToolsMetaBat2 /MaxBin2 /CONCOCT6TiaraGUNCPROKKAMetaEuk89GTDBTK / CATBUSCO / CheckM / CheckM2QUASTShort-read adapter/host/PhiX removal, normalisationLong-read adapter/host/Lambda removal, quality filteringContig binning7Bin refinementBin quality evaluationBin taxonomic classificationand annotationENDMultiQC/Bin Summary10Run summaryShort read taxonomic classificationDe novo assembly, contig evaluation & annotationAncient contig identificationand damage correction diff --git a/docs/images/mag_metromap_simple_dark.png b/docs/images/mag_metromap_simple_dark.png deleted file mode 100644 index ee73c55a..00000000 Binary files a/docs/images/mag_metromap_simple_dark.png and /dev/null differ diff --git a/docs/images/mag_metromap_simple_dark.svg b/docs/images/mag_metromap_simple_dark.svg deleted file mode 100644 index 5eccb751..00000000 --- a/docs/images/mag_metromap_simple_dark.svg +++ /dev/null @@ -1,2047 +0,0 @@ - - - -Nanoplot(Raw)Nanolyse /chopperKraken2 /CentrifugeFiltlong /NanoqchopperNanoplot(Filtered)porechoporporechop_ABIFastQC(Trimmed)FastQC(Raw)Bowtie2 (Host)Run merge Bowtie2(PhiX)BBNormKronaAdapterRemovalorfastp - - -nf-core/magMEGAHIT /SPAdesProdigalQUASTgeNomadpyDamageFreeBayesBCFToolsDASToolMetaBat2 /MaxBin2 / CONCOCTTiaraProkkaMetaEukGUNCMultiQCBin Summary34567fastqfastqfastqfastq1083Short readclassification4Assembly5Ancient DNA6Binning7Bin refinement8Annotation9Contigclassification10Reportgeneration1Short readpreprocessing2Long readpreprocessing12Bowtie2 (Contigs)GTDBTKCATQUAST9Short readsLong readsAssembled contigsGenome binsMultipleparallelchoicesSingle choiceDEFAULTOPT-INBUSCO /CheckM /CheckM2v3.3 diff --git a/docs/images/mag_metromap_simple_light.png b/docs/images/mag_metromap_simple_light.png deleted file mode 100644 index 1ee20624..00000000 Binary files a/docs/images/mag_metromap_simple_light.png and /dev/null differ diff --git a/docs/images/mag_metromap_simple_light.svg b/docs/images/mag_metromap_simple_light.svg deleted file mode 100644 index 3b4011ce..00000000 --- a/docs/images/mag_metromap_simple_light.svg +++ /dev/null @@ -1,2050 +0,0 @@ - - - -Kraken2 /CentrifugeNanoplot(Raw)Nanolyse /chopperFiltlong /NanoqchopperNanoplot(Filtered)porechoporporechop_ABIFastQC(Trimmed)FastQC(Raw)Bowtie2 (Host)Run merge Bowtie2(PhiX)BBNormKronav3.3AdapterRemovalorfastp - - -nf-core/magMEGAHIT /SPAdesProdigalQUASTgeNomadpyDamageFreeBayesBCFToolsDASToolMetaBat2 /MaxBin2 /CONCOCTTiaraProkkaMetaEukGUNCMultiQCBin Summary34567fastqfastqfastqfastq1083Short readclassification4Assembly5Ancient DNA6Binning7Bin refinement8Annotation9Contigclassification10Reportgeneration1Short readpreprocessing2Long readpreprocessing12Bowtie2 (Contigs)BUSCO /CheckM /CheckM2GTDBTKCATQUAST9Short readsLong readsAssembled contigsGenome binsMultipleparalleloptionsSingle choiceDEFAULTOPT-IN