Fix docs and new metro map

Author: matthdsm

CHANGELOG.md

@@ -50,7 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.0.2
 
-- Drop unsed params
+- Drop unused params
 - Set aligner to `star` for RNA-seq
 - Finetune resources
 - Fix some bugs for different input tags

README.md

@@ -18,17 +18,23 @@ It also performs basic QC and coverage analysis.
 
 The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
 
-Steps inlcude:
+Steps include:
 
-1. Demultiplexing using [`BCLconvert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)
-2. Read QC and trimming using [`fastp`](https://github.com/OpenGene/fastp)
-3. Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq
-4. Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html)
-5. Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html)
-6. Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollecHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics)
-7. QC aggregation using [`multiqc`](https://multiqc.info/)
+- Demultiplexing using [`BCLconvert`](https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html)
+- Run QC using [`MultiQC SAV`](https://github.com/MultiQC/MultiQC_SAV)
+- Read QC and trimming using [`fastp`](https://github.com/OpenGene/fastp) or [`falco`](https://github.com/smithlabcode/falco)
+- Alignment using either [`bwa`](https://github.com/lh3/bwa), [`bwa-mem2`](https://github.com/bwa-mem2/bwa-mem2), [`bowtie2`](https://github.com/BenLangmead/bowtie2), [`dragmap`](https://github.com/Illumina/DRAGMAP), [`snap`](https://github.com/amplab/snap) or [`strobe`](https://github.com/ksahlin/strobealign) for DNA-seq and [`STAR`](https://github.com/alexdobin/STAR) for RNA-seq
+- Duplicate marking using [`bamsormadup`](https://gitlab.com/german.tischler/biobambam2) or [`samtools markdup`](http://www.htslib.org/doc/samtools-markdup.html)
+- Coverage analysis using [`mosdepth`](https://github.com/brentp/mosdepth) and [`samtools coverage`](http://www.htslib.org/doc/samtools-coverage.html)
+- Alignment QC using [`samtools flagstat`](http://www.htslib.org/doc/samtools-flagstat.html), [`samtools stats`](http://www.htslib.org/doc/samtools-stats.html), [`samtools idxstats`](http://www.htslib.org/doc/samtools-idxstats.html) and [`picard CollectHsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectHsMetrics), [`picard CollectWgsMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectWgsMetrics), [`picard CollectMultipleMetrics`](https://broadinstitute.github.io/picard/command-line-overview.html#CollectMultipleMetrics)
+- QC aggregation using [`multiqc`](https://multiqc.info/)
 
-![metro map](docs/images/metro_map.png)
+<picture>
+
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/metro_map_dark.svg">
+  <source media="(prefers-color-scheme: light)" srcset="docs/images/metro_map_light.svg">
+  <img alt="Fallback image description" src="docs/images/metro_map_light.svg">
+</picture>
 
 ## Usage
 
@@ -37,36 +43,15 @@ Steps inlcude:
 
 The full documentation can be found [here](docs/README.md)
 
-First, prepare a samplesheet with your input data that looks as follows:
-
-`samplesheet.csv` for fastq inputs:
-
-```csv
-id,samplename,organism,library,aligner,fastq_1,fastq_2
-sample1,sample1,Homo sapiens,Library_Name,bwamem,reads1.fq.gz,reads2.fq.gz
-```
-
-`samplesheet.csv` for flowcell inputs:
-
-```csv
-id,samplesheet,lane,flowcell,sample_info
-flowcell_id,/path/to/illumina_samplesheet.csv,1,/path/to/sequencer_uploaddir,/path/to/sampleinfo.csv
-```
-
-`sampleinfo.csv` for use with flowcell inputs:
-
-```csv
-samplename,library,organism,tag,aligner
-fc_sample1,test,Homo sapiens,WES,bwamem
-```
+First, prepare a samplesheet with your input data. Check the [usage docs](docs/usage.md) for details on the required format and example files.
 
 Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-cmgg/preprocessing \
-   -profile <docker/singularity/.../institute> \
+   -profile <docker/singularity/...> \
    --igenomes_base /path/to/genomes \
-   --input samplesheet.csv \
+   --input samplesheet.<csv|yaml|json> \
    --outdir <OUTDIR>
 ```
 

assets/schema_input.json

@@ -160,10 +160,10 @@
         },
         "anyOf": [
             {
-                "required": ["id", "samplename", "organism", "aligner", "tag", "fastq_1", "fastq_2"]
+                "required": ["id", "samplename", "organism", "aligner", "fastq_1", "fastq_2"]
             },
             {
-                "required": ["id", "samplename", "genome", "aligner", "tag", "fastq_1", "fastq_2"]
+                "required": ["id", "samplename", "genome", "aligner", "fastq_1", "fastq_2"]
             },
             {
                 "required": ["id", "samplesheet", "sample_info", "flowcell"]