Command Log: August 19, 2024, 3:02 pm
curl -o environment.yml 'https://go.unl.edu/nf_env' --location --cookie-jar /tmp/tmp
ls
more environment.yml
module purge
module load miniforge nano
module list
mamba env create -n nf-training -f environment.yml
more environment.yml
clear
ame: nf-training
channels:
ame: nf-training
channels:
- conda-forge
- conda-forge
- bioconda
- bioconda
- salmon=1.10.3
- nextflow=24.04.4
dependencies:
- salmon=1.10.3
- fastqc=0.12.1
dependencies:
- nextflow=24.04.4
- multiqc=1.23
- fastqc=0.12.1
- multiqc=1.23
- nf-core
- nf-core
- nf-core
- nf-core
clear
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
ls
tar -xvf data.tar.gz
ls
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743
clear
pwd
ls
rm data.tar.gz*
rm -rf data*
ls
wget --content-disposition https://ndownloader.figshare.com/files/28531743
ls
tar -xvf data.tar.gz
ls
rm data.tar.gz
ls
wget https://github.com//carpentries-incubator/workflows-nextflow/archive/main.zip
wget https://github.com//carpentries-incubator/workflows-nextflow/archive/main.zip
ls
wget https://github.com//carpentries-incubator/workflows-nextflow/archive/main.zip
wget https://github.com//carpentries-incubator/workflows-nextflow/archive/main.zip
ls
rm main.zip.1
unzip main.zip 'workflows-nextflow-main-episodes/files/scrupts' -d
unzip main.zip 'workflows-nextflow-main-episodes/files/scrupts' -d .
unzip main.zip 'workflows-nextflow-main-episodes/files/scripts' -d .
unzip main.zip 'workflows-nextflow-main/episodes/files/scripts' -d .
ls
unzip main.zip
ls
mv workflows-nextflow-main/episodes/files/scripts/ .
ls
ls scripts/
rm -rf workflows-nextflow-main/
rm main.zip
ls
cpear
clear
pwd
ls
conda activate nf-training
cp scripts/introduction/word_count.nf .
ls
more word_count.nf
more word_count.nf
more word_count.nf
nextflow run word_count.nf
which nextflow
clear
more word_count.nf
nextflow run word_count.nf --input 'data/yeast/reads/ref2_2.fq.gz'
nextflow run word_count.nf --input 'data/yeast/reads/ref2_*.fq.gz'
ls data/yeast/reads/ref2_*.fq.gz
nano word_count.nf
nextflow run word_count.nf
nextflow run word_count.nf --input 'data/yeast/reads/ref2_*.fq.gz'
more word_count.nf
ls data/yeast/reads/ref*.fq.gz
nextflow run word_count.nf --input 'data/yeast/reads/ref*.fq.gz'
cp word_count.nf wc-params.nf
nano wc-params.nf
nextflow run wc-params.nf
nano wc-params.nf
nextflow run wc-params.nf --sleep_today 10
ls data/yeast/reads/*.fq.gz
nextflow run wc-params.nf --sleep_today 10 --input 'data/yeast/reads/*.fq.gz'
nano wc-params.json
nextflow run wc-params.nf -params-file wc-params.json
more wc-params.json
clear