How to...

Matt

How to get the path for the folder containing a bash script within the bash script:

# Get the directory where the script resides
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
echo $SCRIPTDIR

Matt

How to convert a minimap2 alignment to gff/gtf:
https://github.com/lh3/minimap2/issues/455
https://github.com/lh3/minimap2/files/9591008/bam2gff_fixGffread.zip
bam2gff_fixGffread.zip

minimap2 -t 10 -ax splice:hq -uf ref.fa cdna.fa |/Bio/bin/samtools-1.14 view -b > minimap2.tr.bam
perl bam2gff.pl -b minimap2.tr.bam -o minimap2.tr.gff -s /Bio/bin/samtools-1.14 gffread minimap2.tr.gff -T -o minimap2.tr.gtf
perl fixGffread.pl -i minimap2.tr.gtf -o minimap2.tr.fix.gtf

Alternative method:

#Align sequences and convert to BAM
minimap2 -ax splice --cs target.fa query.fa | samtools sort -O BAM - > alignments.bam
#Convert to BED12 using BEDtools
bedtools bamtobed -bed12 -i alignments.bam > alignments.bed 
#Convert to genePred using UCSC tools
bedToGenePred alignments.bed alignments.genepred
#Convert to GTF2 using UCSC tools. genePredToGtf has additional options that might be useful in specific use cases.
genePredToGtf "file" alignments.genepred alignments.gtf

Matt

How to do a dotplot with minimap2:

minimap2 -DP ref.fa query.fa|miniasm/minidot - > dot.eps

Matt

How to interpret genome dot plots (#dotplots #genomic).

interpretation of dotplots.jpg

Matt

How to clone a public GitHub repository with VS Code and push it to a private GitHub repository.

Make sure Git is installed
Open VS Code and use the source control icon on the far left to clone a git repository to a local folder

Open a terminal in VS Code (View>terminal)

PS C:\Users\github> cd sarek
PS C:\Users\github\sarek> git remote remove origin
PS C:\Users\github\sarek> git remote add origin https://github.com/ink-blot/sarek.git
PS C:\Users\github\sarek> git branch
* master
PS C:\Users\github\sarek> git push -u origin master

If it doesn't promptly start pushing, an authorisation screen should (eventually) appear (it may take a few minutes).

The token method is preferred:

Go to your GitHub account settings: GitHub Token Settings.
Click Generate new token (classic).
Select the scopes you need (e.g., repo for private repositories).
Generate the token and copy it (you won’t be able to see it again later).
In the GitHub sign-in window, switch to the Token tab.
Paste the generated token into the input field and confirm.

Optional steps if you want to fetch updates from the original nf-core/sarek repository in the future, add it as an upstream remote:


PS C:\Users\github\sarek> git remote add upstream https://github.com/nf-core/sarek.git
PS C:\Users\github\sarek> git fetch upstream
PS C:\Users\github\sarek> git merge upstream/main

Matt

How to get rid of "WARNING : No mitochondrion chromosome found" in SnpEff:

Prefix the contig name with MT.

Matt

How to collect all files from one channel and associate/combine them with elements of another channel in NextFlow:

Example Input channels:

bam_for_collect_ch2:
[ file('73-50_L002.bam') ]
[ file('73-50_L001.bam') ]

interval_vcfs_3:
[ file('73-50_L001_raw_variants_1.vcf.gz') ]
[ file('73-50_L001_raw_variants_2.vcf.gz') ]
[ file('73-50_L002_raw_variants_1.vcf.gz') ]
[ file('73-50_L002_raw_variants_2.vcf.gz') ]

Process code:

input:
set val(pair_id), val(all_vcf) from bam_for_collect_ch2.map({ file -> file.baseName }).combine(interval_vcfs_3.collect().map({ file -> file.baseName }).toList())

Example output:

[ '73-50_L002', ['73-50_L002_raw_variants_1.vcf.gz', '73-50_L002_raw_variants_2.vcf.gz'] ]
[ '73-50_L001', ['73-50_L001_raw_variants_1.vcf.gz', '73-50_L001_raw_variants_2.vcf.gz'] ]

Matt

How to collect all files related by prefix in NextFlow:

Example input channel:

interval_bams_ch:
[ file('73-50_L001_raw_variants_1.bam') ]
[ file('73-50_L001_raw_variants_2.bam') ]
[ file('73-50_L002_raw_variants_1.bam') ]
[ file('73-50_L002_raw_variants_2.bam') ]

Process code:

bam_name_parts_ch = interval_bams_ch.map { file ->
    def name = file.baseName.replaceFirst(/_raw_variants_.*/, '')
    tuple(name, file)
}.groupTuple()

Example output:

[ '73-50_L001', [file('73-50_L001_raw_variants_1.bam'), file('73-50_L001_raw_variants_2.bam')] ]
[ '73-50_L002', [file('73-50_L002_raw_variants_1.bam'), file('73-50_L002_raw_variants_2.bam')] ]

Matt

How to conditionally choose from two channels in NextFlow:

grouped_interval_vcf_ch=(params.splitIntervalOverlapLength && params.splitIntervalOverlapLength.toInteger() > 0
	? trimmed_vcf_ch
	: interval_vcfs_3
)

Matt

How to re-use a file channel and indeterminate number of times (eg combining with a channle with an unknkown number of elements in NextFlow DSL1:

process collectGVCF {
  publishDir "${params.combined_1_vcf}", mode: 'copy'

  output:
    set val(pair_id), val(round), file("${pair_id}_raw_variants_${round}.vcf.gz") into collected_vcf
}

// Later after splitting:
sample_files
  .map { it -> it.getBaseName() }
  .combine(Channel.fromPath("${params.combined_1_vcf}/*_raw_variants_1.vcf.gz"))
  .set { reuse_pairs }