Commit 3930554f authored by jcorvi's avatar jcorvi

version of components

parent d4a1fb1e
......@@ -33,12 +33,12 @@ profiles {
process {
withName: pretox_sentence_classifier{
container = "javicorvi/stanford-classifier:1.0"
container = "javicorvi/stanford-classifier:1.3"
}
}
process {
withName: nlp_standard_preprocessing{
container = "javicorvi/nlp-standard-preprocessing:1.4"
container = "javicorvi/nlp-standard-preprocessing:develop"
}
}
......@@ -80,7 +80,7 @@ profiles {
process {
withName: ades_ner_postprocessing{
container = "javicorvi/ades-ner-postprocessing:1.2"
container = "javicorvi/ades-ner-postprocessing:1.4.BETA"
}
}
......@@ -92,7 +92,7 @@ profiles {
process {
withName: ades_export_to_json{
container = "javicorvi/ades-export-to-json:1.0"
container = "javicorvi/ades-export-to-json:1.1.BETA"
}
}
......
......@@ -46,6 +46,8 @@ params.folders = [
pdf_to_text_output_folder: "${params.baseDir}/pdf_to_text_output",
//Output directory for the linnaeus tagger step
nlp_standard_preprocessing_output_folder: "${params.baseDir}/nlp_standard_preprocessing_output",
//Output directory for the sentence classification step
sentence_classification_output_folder: "${params.baseDir}/sentence_classification_output",
//Output directory for the linnaeus tagger step
linnaeus_output_folder: "${params.baseDir}/linnaeus_output",
//Output directory for the dnorm tagger step
......@@ -72,6 +74,7 @@ params.folders = [
basedir_input_ch = Channel.fromPath(params.general.inputDir, type: 'dir' )
pdf_to_text_output_folder=file(params.folders.pdf_to_text_output_folder)
nlp_standard_preprocessing_output_folder=file(params.folders.nlp_standard_preprocessing_output_folder)
sentence_classification_output_folder=file(params.folders.sentence_classification_output_folder)
linnaeus_output_folder=file(params.folders.linnaeus_output_folder)
dnorm_output_folder=file(params.folders.dnorm_output_folder)
hepatotoxicity_output_folder=file(params.folders.hepatotoxicity_output_folder)
......@@ -267,16 +270,35 @@ process nlp_standard_preprocessing {
exec >> $pipeline_log
echo "********************************************************************************************************************** "
echo `date`
echo "Start Pipeline Execution, Pipeline Version $pipeline_version, workflow name: ${workflow.runName}"
echo "Start nlp-standard-preprocessing"
nlp-standard-preprocessing -i $input_nlp_standard_preprocessing -o $nlp_standard_preprocessing_output_folder -a BSC -t 8
echo "End nlp-standard-preprocessing"
nlp-standard-preprocessing -i $input_nlp_standard_preprocessing -o $nlp_standard_preprocessing_output_folder -a BSC -t 8 -f true
echo "End nlp-standard-preprocessing"
"""
}
process pretox_sentence_classifier {
input:
file input_sentence_classification from nlp_standard_preprocessing_output_folder_ch
output:
val sentence_classification_output_folder into sentence_classification_output_folder_ch
script:
"""
exec >> $pipeline_log
echo "********************************************************************************************************************** "
echo `date`
echo "Start pretox_sentence_classifier"
stanford-classifier -i $input_sentence_classification -o $sentence_classification_output_folder -a BSC
echo "End pretox_sentence_classifier"
"""
}
process cdisc_etox_annotator {
input:
file input_cdisc_etox from nlp_standard_preprocessing_output_folder_ch
file input_cdisc_etox from sentence_classification_output_folder_ch
output:
val cdisc_etox_output_folder into cdisc_etox_output_folder_ch
......
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