Add variables for usegalaxy.star servers

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# Introduction to sequencing data
## FASTQ manipulation and quality control
## Paired end data
#### Two single files
#### Interleaved file
## What are base qualities?
## Assessing data quality
## Mapping your data
### Mapping against a pre-computed genome index
### What if pre-computed index does not exist?
## SAM/BAM datasets
### SAM Header
### SAM alignment section
### `FLAG` field
### `CIGAR` string
### Optional fields
### Read Groups
### Manipulating SAM/BAM datasets
## The challenge of read duplicates
### PCR duplicates
### Sampling coincidence duplicates
# Getting NGS data to Galaxy
## From your computer
## Using FTP
## From NCBI short read archive
# Let's do it: From reads to variants
## Find necessary data in SRA
## Process and filter `SraRunInfo.csv` file in Galaxy
## Download sequencing data
## Now what?
## Get the reference genome data
## Adapter trimming with **fastp**
## Alignment with  **Map with BWA-MEM**
## Remove duplicates with **MarkDuplicates**
## Generate alignment statistics with **Samtools stats**
## **Realign reads** with lofreq viterbi
## Add indel qualities with lofreq **Insert indel qualities**
## Call Variants using lofreq **Call variants**
## Annotate variant effects with **SnpEff eff: annotate variants for SARS-CoV-2**
## Create table of variants using **SnpSift Extract Fields**
## Summarize data with **MultiQC**
## Collapse data into a single dataset
## Anything interesting?
# Let's do it: A peek at secondary analysis in Galaxy
# Let's do it: A peek at secondary analysis in Google Colab
# Conclusion

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