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Makefile
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Makefile
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PROJECT_NAME = TNBC_PRED # Project name
VERSION = 1 # Project version
LABEL_FILE = ./outputs/label.csv # Label name
PROFILE = mines #nextflow profile, us it was the mine cluster profile
DATA_PATH = ../Data/TNBC_biopsy/ # /path/to/tiff
TISSUE_SEGMENTATION = ../Data/TNBC_biopsy/tissue_segmentation # /path/to/wsi/tissue/masks
RESOLUTIONS = 0 1 2 # Resolution to investigate
Y_TARGETS = Residual Prognostic # Name of y targets that can be found in LABEL_FILE
$(LABEL_FILE):
CSV_DATA1 = ../Data/Biopsy_csv/rcb_substrat.csv
PATH_DATA1 = ../Data/Biopsy_guillaume
OUT_DATA1 = ../Data/Biopsy_csv/rcb_substrat_after.csv
XLSX_DATA2 = ../Data/Biopsy_csv/MarickDataSet.xlsx
PATH_DATA2 = ../Data/Biopsy/
OUT_DATA2 = ../Data/Biopsy_csv/ftnbc.csv
python python/label_standardise/substrat_label.py --input_table $(CSV_DATA1) \
--folder_to_check $(PATH_DATA1) \
--output_table $(OUT_DATA1)
python python/label_standardise/ftnbc_label.py --input_table $(XLSX_DATA2) \
--folder_to_check $(PATH_DATA2) \
--output_table $(OUT_DATA2)
python python/label_standardise/create_test_folds.py --substra $(OUT_DATA1) \
--ftnbc $(OUT_DATA2) \
--output_name $(LABEL_FILE)
ln -s LINK
ln -sr $(PATH_DATA1)/* $(DATA_PATH)/
encoding: $(LABEL_FILE)
nextflow run nextflow/Tiling-encoding.nf -resume -c ~/.nextflow/config -profile $(PROFILE) \
--tiff_location $(DATA_PATH)/ \
--PROJECT_NAME $(PROJECT_NAME) --PROJECT_VERSION $(VERSION) \
--tissue_bound_annot $(TISSUE_SEGMENTATION) \
--label $(LABEL_FILE)
model_2S: $(LABEL_FILE)
for y_interest in $(Y_TARGETS)
do
for res in $(RESOLUTIONS)
do
echo "####################################################################"
echo
echo "########### Doing ${y_interest} at ${res} ###############"
echo
echo "####################################################################"
nextflow run nextflow/Model_2S.nf -resume -c ~/.nextflow/config -profile $(PROFILE) \
--PROJECT_NAME $(PROJECT_NAME) --PROJECT_VERSION $(PROJECT_VERSION) \
--resolution $res --y_interest ${y_interest} \
--label $(LABEL_FILE)
done
done
model_1S: $(LABEL_FILE)
for y_interest in $(Y_TARGETS)
do
for res in $(RESOLUTIONS)
do
if [ $res -eq 0 ]
then
size=5000
else
if [ $res -eq 1 ]
then
size=3000
else
size=1000
fi
fi
echo "####################################################################"
echo
echo "########### Doing ${y_interest} at ${res} input size $size ###############"
echo
echo "####################################################################"
nextflow run nextflow/Model_nn.nf -resume -c ~/.nextflow/config -profile $(PROFILE) \
--PROJECT_NAME $(PROJECT_NAME) --PROJECT_VERSION $(VERSION) \
--resolution $res --y_interest ${y_interest} \
--label $(LABEL_FILE) \
--input_tiles ./outputs/$(PROJECT_NAME)_$(PROJECT_VERSION)/tiling/${res}/mat_pca/ \
--mean ./outputs/$(PROJECT_NAME)_$(PROJECT_VERSION)/tiling/${res}/pca_mean/mean.npy
done
done
repeated_experiment:
nextflow run nextflow/Repeated_experiment.nf -resume
necv_vs_ncv:
nextflow run nextflow/NECV_VS_NCV.nf -resume