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demux.wdl
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demux.wdl
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version 1.0
workflow demux {
input {
File infastq
File reads
File pythonscript
String barcodekit
}
call guppybarcoder {
input:
infastq=infastq,
barcodekit=barcodekit
}
call makefast5s {
input:
reads=reads,
pythonscript=pythonscript,
barcoding_summary = guppybarcoder.barcoding_summary
}
call makesheet {
input:
fastqs = guppybarcoder.fastqs,
fast5_tars = makefast5s.fast5_tars
}
output {
File samplesheet=makesheet.samplesheet
Array[File] fast5_tars = makefast5s.fast5_tars
Array[File] fastqs = guppybarcoder.fastqs
}
meta {
author: "Mark Soliman"
email:"[email protected]"
}
}
task guppybarcoder {
input {
File infastq
String barcodekit
}
command <<<
mkdir out
mkdir in
cp ~{infastq} ./in
guppy_barcoder -i ./in -s ./out ~{barcodekit} #--enable_trim_barcodes
for f in ./out/*; do
dir_name="${f##*/}"
cat "$f"/*.fastq > ./out/"$dir_name".fastq
# for file in "$f"/*.fastq; do
# mv "$file" "$f/$dir_name-${file##*/}"
# done
done
column=$(head -n 2 ./out/barcoding_summary.txt | tail -n 1 | awk -F$'\t' 'BEGIN{search="unclassified|barcode"} { for (i=1; i<=NF; i++) { if ($i ~ search) print i } }')
cat ./out/barcoding_summary.txt | cut -f 1,${column} >> ./out/twocolumnsummary.tsv
>>>
runtime {
docker: "us-central1-docker.pkg.dev/aryeelab/docker/megalodon"
memory: "64 GB"
disks: "local-disk 1000 SSD"
cpu: 12
}
output {
File barcoding_summary = "./out/twocolumnsummary.tsv"
Array[File] fastqs = glob("./out/*.fastq")
}
}
task makefast5s {
input {
File reads
File pythonscript
File barcoding_summary
}
command <<<
filetype=$(file ~{reads})
mkdir in
if [[ ~{reads} == *.pod5 ]]; then
pod5 convert to_fast5 ~{reads} --output ./in
else
tar xvzf ~{reads} -C ./in
fi
mkdir out
column_name=$(awk -F'\t' 'NR==1 {print $2}' ~{barcoding_summary})
python3 ~{pythonscript} --input ./in --save_path ./out --summary_file ~{barcoding_summary} --demultiplex_column ${column_name}
for f in ./out/*; do tar czvf "$f.tar.gz" "$f"/*.fast5; done
>>>
runtime {
docker: "us-central1-docker.pkg.dev/aryeelab/docker/ontfast5api"
memory: "64 GB"
disks: "local-disk 1000 SSD"
cpu: 12
}
output {
Array[File] fast5_tars= glob("./out/*.tar.gz")
}
}
task makesheet {
input {
Array[String] fastqs
Array[String] fast5_tars
}
command <<<
echo fastq_gz ~{sep=' ' fastqs} >> samples_t.txt
echo fast5_tar ~{sep=' ' fast5_tars} >> samples_t.txt
cat samples_t.txt | datamash --output-delimiter=',' -t ' ' transpose > samples.csv
>>>
runtime {
docker: "quay.io/aryeelab/nanopore-util"
memory: "64 GB"
disks: "local-disk 1000 SSD"
cpu: 12
}
output {
File samplesheet= "samples.csv"
}
}