Prepare participants' data shared on dropbox

[tavareshugo]

The participants' data will go in their own dropbox folder. Each of the participants' data needs to follow the same directory structure as all other eqa_* folders:

• data/reads --> with FASTQ files
• resources --> with pre-downloaded resources
• README.txt --> with details about platform and primer scheme
• scripts --> with the R scripts (not the shell scripts, because those they create as part of the exercises)
• sample_info.csv --> some metadata provided by the institution

[tavareshugo]

Data for this workshop iteration:

wget -O eqa_nanopore_dataset1.zip "https://www.dropbox.com/scl/fo/732l7klvyjfmusitrccjw/h?rlkey=729c7bu5knhd9ecf159ygchb8&dl=1"
wget -O eqa_nanopore_dataset2.zip "https://www.dropbox.com/scl/fo/qqs9dkzdp336spgsbjeuh/h?rlkey=851ze3qmcsiqf71hr9u9p638a&dl=1"
wget -O eqa_nanopore_dataset3.zip "https://www.dropbox.com/scl/fo/kizqz3buhtsmpoo9e7x8r/h?rlkey=9nuv5er4y3si5u38ekb89cvo1&dl=1"
wget -O eqa23_illumina_dataset1.zip "https://www.dropbox.com/scl/fo/3kwxinsxlwdtp2a1osugf/h?rlkey=mebutply5to1chrjjwyo76j01&dl=1"
wget -O eqa23_illumina_dataset2.zip "https://www.dropbox.com/scl/fo/cy7zu5cjs1relqfnqfgia/h?rlkey=r49oti78cwl2j5oc366btvlu1&dl=1"
wget -O eqa23_illumina_dataset3.zip "https://www.dropbox.com/scl/fo/4gcj25il1tmqotyjp1l3w/h?rlkey=wbyxuyjqv0dbmatda479uqy36&dl=1"
wget -O switzerland_nanopore_small.zip "https://www.dropbox.com/scl/fo/y37yqean6vamzr7yq8zey/h?rlkey=qdavkteytx8inv0qpvai11lby&dl=1"
wget -O southafrica_illumina_small.zip "https://www.dropbox.com/scl/fo/lbw1eucabhrd26ce4xf1j/h?rlkey=aelkvldj1hta8xaqnqzkydb7v&dl=1"

Unzip all of them:

for i in *.zip
do
  unzip $i -d $(basename $i ".zip")
done

rm *.zip

[tavareshugo]

Remove large files from pre-processed dirs

[liamxg]

what is the different between wget -O and curl -O?