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