How to...

Matt

How to login to root account in a new ubuntu/xubuntu virtual machine that has been set up with a non-administrator account:

su
yourpasswordfortheuseraccount

Matt

How to update apt and install filezilla on xubuntu using a proxy:

sudo apt -o Acquire::http::proxy="http://user:password@host:port/" update
sudo apt -o Acquire::http::proxy="http://user:password@host:port/" install filezilla

Matt

How to install ubuntu on windows:

Follow the instructions at:
https://s1gr1d.medium.com/how-to-set-up-linux-on-windows-with-wsl-2-debe2a64d20d
(NB. these instructions work for Windows 10 and 11 although the location of the Settings menus may differ slightly. Also note that VMX is the same as VT-X in the BIOS settings)
In Windows Powershell, you may also need to issue the following commands:

bcdedit /set hypervisorlaunchtype Auto
wsl --update

Matt

How to use your phone as a webcam:

https://www.youtube.com/watch?v=ArVDKf2QK1s

Matt

How to fix the following error in NextFlow:

WARN: Failed to render DAG file:

This error prevents NextFlow from drawing the DAG for the pipeline.

#install Graphviz 
#eg. with conda
conda install -c conda-forge graphviz

Matt

How to gather and group all tuple elements in a NextFlow channel by the first and second indexes of each tuple, perform a process on a file containing the first and second indices, and then reform the original channel by scattering:

hc_ch = Channel.of(
    ['abc', 1, file('file1.txt')],
    ['abc', 1, file('file2.txt')],
    ['abc', 1, file('file3.txt')],
    ['def', 2, file('file4.txt')]
)

combinedChannel = hc_ch.groupTuple(by: [0, 1])

Expected structure of combinedChannel:

[ ['abc', 1, [file('file1.txt'), file('file2.txt'), file('file3.txt')]],
['def', 2, [file('file4.txt')]]
]


process delete_txt {

    input:
    tuple val(id), val(sub_id), val(files) from combinedChannel

    output:
    tuple val(id), val(sub_id), val(files) into processedChannel

    script:
    """
    rm ${id}_${sub_id}.txt
    """
}

Expected structure of processedChannel:

[ ['abc', 1, [file('file1.txt'), file('file2.txt'), file('file3.txt')]],
['def', 2, [file('file4.txt')]]
]

flattenedChannel = processedChannel.flatMap { id, sub_id, files -> files.collect { [id, sub_id, it] } }

Expected structure of flattenedChannel:
[ ['abc', 1, file('file1.txt')],
['abc', 1, file('file2.txt')],
['abc', 1, file('file3.txt')],
['def', 2, file('file4.txt')]
]

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 }

Matt

How to apply for a Visa on Arrival for Indonesia online before you travel:

A Visa on Arrival (VOA) is available for passport holders in many countries including Australia. It costs US$35 (A$50) and is valid for 30 days. Follow the link below to apply.

https://evisa.imigrasi.go.id/

Matt

How to show fold changes in an excel spreadsheet when there are 0 values in the denominator. In the example below P30 is the numerator and P2 is the denominator. The logic is:

Both numerator and denominator = 0 → output 0.00
Denominator = 0, numerator ≠ 0 → output >{numerator} (2 decimals)
Numerator = 0, denominator ≠ 0 → output <{denominator} (2 decimals)
Otherwise → output normal division with 2 decimals.

=IF(AND(P30=0,P2=0),"0.00",
   IF(P2=0,">"&TEXT(P30,"0.00"),
      IF(P30=0,"<"&TEXT(P2,"0.00"),
         TEXT(P30/P2,"0.00"))))

Matt

How to search for a file on linux and suppress error messages and stop once the first instance is found:

find /home/files -xdev -type f -name 'P13.txt' -print -quit 2>/dev/null

Matt

How to withdraw money from a Commonwealth Bank ATM using your phone and the CommBank App.

On the ATM screen, select “Cardless Cash”
In the CommBank app go to 'Pay' > 'Cardless Withdrawal & Deposit ".
Using your phone, scan the QR code on the ATM screen.