Merge pull request #150 from Joon-Klaps/update-docs

Update docs

Author: Joon-Klaps

.github/workflows/build-docs.yml

@@ -2,7 +2,6 @@ name: Publish Docs On Change
 on:
   push:
     branches:
-      - main
       - dev
       - master
   workflow_dispatch:
@@ -45,15 +44,19 @@ jobs:
       - name: Read parameter tip
         id: read_tip
         run: |
-          tip=$(cat docs/parameter_tip.txt)
+          tip=$(cat docs/parameter_tip.md)
           echo "tip_content=$tip" >> $GITHUB_ENV
       - name: Append content to parameters.md
         run: |
           modified_content=$(awk '/^#/ { print; print "${{ env.tip_content }}"; exit } 1' docs/parameters.md)
           echo "$modified_content" > docs/parameters.md
       - name: Build docs
         run: |
-          RELEASE=$(curl -sL https://api.github.com/repos/Joon-Klaps/viralgenie/releases | jq -r '.[0].tag_name')
-          echo "${RELEASE}"
-          mike deploy --push --update-aliases "${RELEASE}" latest
-          mike set-default --push latest
+          if [[ "${{ github.ref }}" == "refs/heads/dev" ]]; then
+            mike deploy --push --update-aliases "dev" dev
+          else
+            RELEASE=$(curl -sL https://api.github.com/repos/Joon-Klaps/viralgenie/releases | jq -r '.[0].tag_name')
+            echo "${RELEASE}"
+            mike deploy --push --update-aliases "${RELEASE}" latest
+            mike set-default --push latest
+          fi

CHANGELOG.md

@@ -19,6 +19,7 @@ Initial release of Joon-Klaps/viralgenie, created with the [nf-core](https://nf-
 - Add logic to allow samples with no reference hits to be analysed ([#141](https://github.com/Joon-Klaps/viralgenie/pull/141))
 - Add visualisation for hybrid scaffold ([#143](https://github.com/Joon-Klaps/viralgenie/pull/143))
 - Add new module to inculde custom mpileup-vcf file for intra-host analyses ([#151](https://github.com/Joon-Klaps/viralgenie/pull/151))
+- Update docs ([#150](https://github.com/Joon-Klaps/viralgenie/pull/150))
 
 
 ### `Fixed`

README.md

@@ -26,7 +26,7 @@
 
 ## Pipeline summary
 
-![viralgenie-workflow](docs/images/metromap_style_pipeline_workflow_viralgenie.png)
+![viralgenie-workflow](docs/images/metromap_style_pipeline_workflow_viralgenie.svg)
 
 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 2. Performs optional read pre-processing
@@ -37,36 +37,38 @@
 3. Metagenomic diveristy mapping
     - Performs taxonomic classification and/or profiling using one or more of:
         - [`Kraken2`](https://ccb.jhu.edu/software/kraken2/)
-        - [`Bracken`](https://ccb.jhu.edu/software/bracken/)[optional]
+        - [`Bracken`][https://ccb.jhu.edu/software/bracken/](optional)
         - [`Kaiju`](https://kaiju.binf.ku.dk/)
     - Plotting Kraken2 and Kaiju ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))
 4. Denovo assembly ([`SPAdes`](http://cab.spbu.ru/software/spades/), [`TRINITY`](https://github.com/trinityrnaseq/trinityrnaseq), [`megahit`](https://github.com/voutcn/megahit)), combine contigs.
 5. [Optional] extend the contigs with [sspace_basic](https://github.com/nsoranzo/sspace_basic) and filter with [`prinseq++`](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus)
-6. Contig reference idententification ([`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch))
-    -   Identify top 5 blast hits
-    -   Merge blast hit and all contigs of a sample
-7. [Optional] Precluster contigs based on taxonomy
+6. [Optional] Map reads to contigs for coverage estimation ([`BowTie2`](http://bowtie-bio.sourceforge.net/bowtie2/),[`BWAmem2`](https://github.com/bwa-mem2/bwa-mem2) and [`BWA`](https://github.com/lh3/bwa))
+7. Contig reference idententification ([`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch))
+    - Identify top 5 blast hits
+    - Merge blast hit and all contigs of a sample
+8. [Optional] Precluster contigs based on taxonomy
     - Identify taxonomy [`Kraken2`](https://ccb.jhu.edu/software/kraken2/) and\or [`Kaiju`](https://kaiju.binf.ku.dk/)
     - Resolve potential inconsistencies in taxonomy & taxon filtering | simplification `bin/extract_precluster.py`
-8. Cluster contigs (or every taxonomic bin) of samples, options are:
+9. Cluster contigs (or every taxonomic bin) of samples, options are:
     - [`cdhitest`](https://sites.google.com/view/cd-hit)
     - [`vsearch`](https://github.com/torognes/vsearch/wiki/Clustering)
     - [`mmseqs-linclust`](https://github.com/soedinglab/MMseqs2/wiki#linear-time-clustering-using-mmseqs-linclust)
     - [`mmseqs-cluster`](https://github.com/soedinglab/MMseqs2/wiki#cascaded-clustering)
     - [`vRhyme`](https://github.com/AnantharamanLab/vRhyme)
     - [`Mash`](https://github.com/marbl/Mash)
-9. Scaffolding of contigs to centroid ([`Minimap2`](https://github.com/lh3/minimap2), [`iVar-consensus`](https://andersen-lab.github.io/ivar/html/manualpage.html))
-10. [Optional] Annotate 0-depth regions with external reference `bin/lowcov_to_reference.py`.
-11. [Optional] Select best reference from `--mapping_constrains`:
+10. [Optional] Remove clusters with low read coverage. `bin/extract_clusters.py`
+11. Scaffolding of contigs to centroid ([`Minimap2`](https://github.com/lh3/minimap2), [`iVar-consensus`](https://andersen-lab.github.io/ivar/html/manualpage.html))
+12. [Optional] Annotate 0-depth regions with external reference `bin/lowcov_to_reference.py`.
+13. [Optional] Select best reference from `--mapping_constrains`:
     - [`Mash sketch`](https://github.com/marbl/Mash)
     - [`Mash screen`](https://github.com/marbl/Mash)
-12. Mapping filtered reads to supercontig and mapping constrains([`BowTie2`](http://bowtie-bio.sourceforge.net/bowtie2/),[`BWAmem2`](https://github.com/bwa-mem2/bwa-mem2) and [`BWA`](https://github.com/lh3/bwa))
-13. [Optional] Deduplicate reads ([`Picard`](https://broadinstitute.github.io/picard/) or if UMI's are used [`UMI-tools`](https://umi-tools.readthedocs.io/en/latest/QUICK_START.html))
-14. Variant calling and filtering ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html),[`iVar`](https://andersen-lab.github.io/ivar/html/manualpage.html))
-15. Create consensus genome ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html),[`iVar`](https://andersen-lab.github.io/ivar/html/manualpage.html))
-16. Repeat step 12-15 multiple times for the denovo contig route
-17. Consensus evaluation and annotation ([`QUAST`](http://quast.sourceforge.net/quast),[`CheckV`](https://bitbucket.org/berkeleylab/checkv/src/master/),[`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi), [`mmseqs-search`](https://github.com/soedinglab/MMseqs2/wiki#batch-sequence-searching-using-mmseqs-search))
-18. Result summary visualisation for raw read, alignment, assembly, variant calling and consensus calling results ([`MultiQC`](http://multiqc.info/))
+14. Mapping filtered reads to supercontig and mapping constrains([`BowTie2`](http://bowtie-bio.sourceforge.net/bowtie2/),[`BWAmem2`](https://github.com/bwa-mem2/bwa-mem2) and [`BWA`](https://github.com/lh3/bwa))
+15. [Optional] Deduplicate reads ([`Picard`](https://broadinstitute.github.io/picard/) or if UMI's are used [`UMI-tools`](https://umi-tools.readthedocs.io/en/latest/QUICK_START.html))
+16. Variant calling and filtering ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html),[`iVar`](https://andersen-lab.github.io/ivar/html/manualpage.html))
+17. Create consensus genome ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html),[`iVar`](https://andersen-lab.github.io/ivar/html/manualpage.html))
+18. Repeat step 12-15 multiple times for the denovo contig route
+19. Consensus evaluation and annotation ([`QUAST`](http://quast.sourceforge.net/quast),[`CheckV`](https://bitbucket.org/berkeleylab/checkv/src/master/),[`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi), [`mmseqs-search`](https://github.com/soedinglab/MMseqs2/wiki#batch-sequence-searching-using-mmseqs-search), [`MAFFT` - alignment of contigs vs iterations & consensus](https://mafft.cbrc.jp/alignment/software/))
+20. Result summary visualisation for raw read, alignment, assembly, variant calling and consensus calling results ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
@@ -112,10 +114,9 @@ Viralgenie was originally written by [`Joon-Klaps`](https://github.com/Joon-Klap
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
--   [`Philippe Lemey`](https://github.com/plemey)
--   [`Liana Kafetzopoulou`](https://github.com/LianaKafetzopoulou)
--   [`nf-core community`](https://nf-co.re/)
-
+- [`Philippe Lemey`](https://github.com/plemey)
+- [`Liana Kafetzopoulou`](https://github.com/LianaKafetzopoulou)
+- [`nf-core community`](https://nf-co.re/)
 
 ## Contributions and Support
 
@@ -130,8 +131,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- If you use nf-core/viralgenie for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 >[!WARNING]
 > Viralgenie is currently not Published. Please cite as:
-> Klaps J, Lemey P, Kafetzopoulou L. Viralgenie: A metagenomics analysis pipeline for eukaryotic viruses. __Github__ https://github.com/Joon-Klaps/viralgenie
-
+> Klaps J, Lemey P, Kafetzopoulou L. Viralgenie: A metagenomics analysis pipeline for eukaryotic viruses. **Github** <https://github.com/Joon-Klaps/viralgenie>
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](https://joon-klaps.github.io/viralgenie/latest/CITATIONS) file.
 

bin/custom_multiqc.py

@@ -499,11 +499,11 @@ def main(argv=None):
     mqc.parse_logs(args.multiqc_files, args.multiqc_config, ignore_samples=generate_ignore_samples(mqc_custom_df))
 
     # 4. Parse our custom files into the correct tables
-    custom_tables, cluster_df = load_custom_data(args)
+    overview_tables, cluster_df = load_custom_data(args)
 
     # 5. Make our own summary files
     # 5.1 Join with the custom contig tables
-    mqc_custom_df = join_df(mqc_custom_df, custom_tables)
+    mqc_custom_df = join_df(mqc_custom_df, overview_tables)
 
     if mqc_custom_df.empty:
         logger.warning("No data was found to create the contig overview table!")