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Test_15: Pipeline
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@AndreRico
AndreRico committed Oct 21, 2024
1 parent b53c41c commit 628342c
Showing 1 changed file with 114 additions and 64 deletions.
178 changes: 114 additions & 64 deletions pipeline/PharmCAT_Pipeline.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -27,16 +27,17 @@ workflow pharmcat_pipeline {
max_memory = max_memory,
}

# call cloud_writer_task {
# input:
# results = pipeline_task.results,
# }
call cloud_writer_task {
input:
pipeline_results = pipeline_task.pipeline_results,
}


output {
# File results = pipeline_task.results
File cloud_reader_results = cloud_reader_task.cloud_reader_results
File results = pipeline_task.pipeline_results
File pipeline_results = pipeline_task.pipeline_results
File log = cloud_writer_task.log
}
}

Expand Down Expand Up @@ -267,17 +268,60 @@ task pipeline_task {
# Variant Call Format (VCF) Version >= 4.2.

# Resolver a variável `vcf_file` fora do bloco condicional
# Nao podemos usar a variavel `vcf_file` dentro do bloco condicional
vcf_file="~{vcf_file}"

# Obter a extensão do arquivo para verificar se é um arquivo de lista ou um VCF simples
file_extension="${vcf_file##*.}"

# option 1: User add on VCF or TSV file in the vcf_file input
if [[ -n "$vcf_file" && -f "$vcf_file" ]]; then
# if [[ -n ~{vcf_file} && -f ~{vcf_file} ]]; then
# mkdir -p data
cp ~{vcf_file} wf/data
# cp ~{vcf_file} wf/data
# echo "Processing list of VCF files as a single block from: ~{vcf_file}" >> $log_file
# cmd="pharmcat_pipeline wf/data/$(basename ~{vcf_file}) $arg"
# echo "Running command: $cmd" >> $log_file
# eval $cmd

echo "Processing list of VCF files as a single block from: ~{vcf_file}" >> $log_file
cmd="pharmcat_pipeline wf/data/$(basename ~{vcf_file}) $arg"
echo "Running command: $cmd" >> $log_file
eval $cmd

if [[ "$file_extension" == "txt" || "$file_extension" == "tsv" ]]; then
echo "Treatment pathway from : $vcf_file" >> $log_file

# Copiar o arquivo de lista para a pasta interna 'wf/data'
cp "$vcf_file" wf/data
list_file="wf/data/$(basename "$vcf_file")"

# Criar um novo arquivo de lista com o caminho completo 'wf/data/'
adjusted_list="wf/data/adjusted_list.txt"
touch $adjusted_list

# Verificar cada linha no arquivo original e adicionar 'wf/data/' caso necessário
while read -r line; do
if [[ "$line" == wf/data/* ]]; then
# Se a linha já contém 'wf/data/', adicionar diretamente
echo "$line" >> $adjusted_list
else
# Caso contrário, adicionar o prefixo 'wf/data/'
echo "wf/data/$line" >> $adjusted_list
fi
done < "$list_file"

echo "Adjusted VCF list created at: $adjusted_list" >> $log_file

# Rodar o PharmCAT com a lista ajustada
cmd="pharmcat_pipeline $adjusted_list $arg"
echo "Running command: $cmd" >> $log_file
eval $cmd

else
# Caso seja um arquivo VCF simples, processá-lo diretamente
echo "Processing single VCF file: $vcf_file" >> $log_file
cp "$vcf_file" wf/data
cmd="pharmcat_pipeline wf/data/$(basename "$vcf_file") $arg"
echo "Running command: $cmd" >> $log_file
eval $cmd
fi


# Option 2: None VCF or TSV input. Check directory content to process
elif [[ -z "$vcf_file" ]]; then
Expand All @@ -304,7 +348,6 @@ task pipeline_task {
fi



# Run the command
echo "Pharmcat_pipeline finished" >> $log_file

Expand All @@ -324,55 +367,62 @@ task pipeline_task {
}


# task cloud_writer_task {
# input {
# File? result_vcf_preprocessor
# String? results_directory
# }
# command <<<
# set -e -x -o pipefail
# # Extract the compressed file from a_cloud_reader_task
# tar -xzvf ~{result_vcf_preprocessor}
# # Start log file
# log_file="files/log.txt"
# echo " " >> $log_file
# echo "-----------------------" >> $log_file
# echo "Start Cloud Writer Task" >> $log_file
# echo "-----------------------" >> $log_file
# # Ensure gsutil is available in this environment
# if ! command -v gsutil &> /dev/null; then
# echo "ERROR: gsutil not found. Please ensure gsutil is available." >> $log_file
# exit 1
# fi
# # Save Results in directory defined by the user
# echo "Copying results to ~{results_directory}" >> $log_file
# # TODO - Add other cloud directories
# if [[ ~{results_directory} == gs://* ]]; then
# # Copying individual result files
# gsutil cp Results/* "~{results_directory}/" >> $log_file
# # Copying the pre_processor tar.gz as well
# gsutil cp ~{result_vcf_preprocessor} ~{results_directory}/ >> $log_file
# else
# echo "ERROR: Unsupported storage destination. Only gs:// is supported in this task." >> $log_file
# exit 1
# fi
# echo "Cloud Writer Task completed successfully." >> $log_file
# >>>
# output {
# File log = "files/log.txt"
# }
# runtime {
# docker: "ricoandre/cloud-tools:latest"
# memory: "4G"
# cpu: 1
# }
# }
task cloud_writer_task {
input {
File? pipeline_results
String? results_directory
}

command <<<
set -e -x -o pipefail

# Extract the compressed file from a_cloud_reader_task
tar -xzvf ~{pipeline_results}

# Start log file
log_file="wf/log.txt"
echo " " >> $log_file
echo "-----------------------" >> $log_file
echo "Start Cloud Writer Task" >> $log_file
echo "-----------------------" >> $log_file

results_directory="~{results_directory}"

if [[ -z "$results_directory" ]]; then
# Ensure gsutil is available in this environment
if ! command -v gsutil &> /dev/null; then
echo "ERROR: gsutil not found. Please ensure gsutil is available." >> $log_file
exit 1
fi

# Save Results in directory defined by the user
echo "Copying results to ~{results_directory}" >> $log_file

# TODO - Add other cloud directories
if [[ ~{results_directory} == gs://* ]]; then
# Copying individual result files
gsutil cp Results/* "~{results_directory}/" >> $log_file
# Copying the pre_processor tar.gz as well
gsutil cp ~{pipeline_results} ~{results_directory}/ >> $log_file
else
echo "ERROR: Unsupported storage destination. Only gs:// is supported in this task." >> $log_file
exit 1
fi

echo "Cloud Writer Task completed successfully." >> $log_file
else
echo "No results directory defined. Skipping cloud write." >> $log_file
fi

>>>

output {
File log = "wf/log.txt"
}

runtime {
docker: "ricoandre/cloud-tools:latest"
memory: "4G"
cpu: 1
}
}

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