Update README.md

Just some cosmetics/consistency things.

README.md

@@ -24,33 +24,33 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-![nf-core/rnaseq metro map](docs/images/metatdenovo.png)
+![nf-core/metatdenovo metro map](docs/images/metatdenovo.png)
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
-3. Quality trimming and adapters removal for raw reads [`Trimm Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
-4. Filter sequences with [`BBduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/)
-5. Normalize the sequencing depth with [`BBnorm`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/)
-6. Merge trimmed, pair-end reads ( [`Seqtk`](https://github.com/lh3/seqtk))
+3. Quality trimming and adapter removal for raw reads ([`Trimm Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
+4. Optional: Filter sequences with [`BBduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/)
+5. Optional: Normalize the sequencing depth with [`BBnorm`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/)
+6. Merge trimmed, pair-end reads ([`Seqtk`](https://github.com/lh3/seqtk))
 7. Choice of de novo assembly programs:
-   1. [`RNAspade`](https://cab.spbu.ru/software/rnaspades/) suggested for Eukaryotes de novo assembly
+   1. [`RNAspades`](https://cab.spbu.ru/software/rnaspades/) suggested for Eukaryotes de novo assembly
    2. [`Megahit`](https://github.com/voutcn/megahit) suggested for Prokaryotes de novo assembly
 8. Choice of orf caller:
    1. [`TransDecoder`](https://github.com/TransDecoder/TransDecoder) suggested for Eukaryotes
    2. [`Prokka`](https://github.com/tseemann/prokka) suggested for Prokaryotes
    3. [`Prodigal`](https://github.com/hyattpd/Prodigal) suggested for Prokaryotes
 9. Quantification of genes identified in assemblies:
-   1. generate index of assembly [`BBmap index`](https://sourceforge.net/projects/bbmap/)
-   2. Mapping cleaned reads to the assembly for quantification [`BBmap`](https://sourceforge.net/projects/bbmap/)
-   3. Get raw counts per each gene present in the assembly [`Featurecounts`](http://subread.sourceforge.net) -> TSV table with collected featurecounts output
+   1. Generate index of assembly ([`BBmap index`](https://sourceforge.net/projects/bbmap/))
+   2. Mapping cleaned reads to the assembly for quantification ([`BBmap`](https://sourceforge.net/projects/bbmap/))
+   3. Get raw counts per each gene present in the assembly ([`Featurecounts`](http://subread.sourceforge.net)) -> TSV table with collected featurecounts output
 10. Functional annotation:
     1. [`Eggnog`](https://github.com/eggnogdb/eggnog-mapper) -> Reformat TSV output "eggnog table"
     2. [`KOfamscan`](https://github.com/takaram/kofam_scan)
     3. [`HMMERsearch`](https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch) -> Ranking orfs based on HMMprofile with [`Hmmrank`](https://github.com/erikrikarddaniel/hmmrank)
 11. Taxonomic annotation:
     1. [`EUKulele`](https://github.com/AlexanderLabWHOI/EUKulele) -> Reformat TSV output "Reformat_tax.R"
     2. [`CAT`](https://github.com/dutilh/CAT)
-12. Summary statistics table. Collect_stats.R
+12. Summary statistics table. "Collect_stats.R"
 
 ## Usage