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remove prom from models in tests
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@Psy-Fer
Psy-Fer committed Oct 30, 2024
1 parent 4754628 commit 91836b8
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Showing 16 changed files with 28 additions and 28 deletions.
2 changes: 1 addition & 1 deletion test/dorado/test.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/NA12878_prom_subsub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/NA12878_prom_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r9.4.1_450bps_fast_prom.cfg
test -z $MODEL && MODEL=dna_r9.4.1_450bps_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
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2 changes: 1 addition & 1 deletion test/dorado/test_demux.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test -z $BARCODE && BARCODE=SQK-NBD114-96
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
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2 changes: 1 addition & 1 deletion test/dorado/test_demux_qscore_split.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test -z $BARCODE && BARCODE=SQK-NBD114-96
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
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14 changes: 7 additions & 7 deletions test/dorado/test_extensive.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -51,23 +51,23 @@ export REFIDX=/genome/hg38noAlt.idx
echo "R9.4.1 DNA - FAST model - 20k reads"
export PATH_TO_FAST5=/data/slow5-testdata/NA12878_prom_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/NA12878_prom_subsubsample/reads.blow5
export MODEL=dna_r9.4.1_450bps_fast_prom.cfg
export MODEL=dna_r9.4.1_450bps_fast.cfg
test/dorado/test.sh &> r9_dna_fast.log || die "test failed. see r9_dna_fast.log for details"
echo ""
echo "********************************************************************"

echo "R10.4.1 DNA - HAC model - 20k reads - split qscore inbuilt"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test/dorado/test_qscore_split.sh &> r10_split1.log || die "test failed. see r10_split1.log for details"
echo ""
echo "********************************************************************"

echo "R10.4.1 DNA - FAST model - 20k reads - split qscore script"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test/dorado/test_qscore_split2.sh &> r10_split2.log || die "test failed. See r10_split2.log for details"
echo ""
echo "********************************************************************"
Expand Down Expand Up @@ -127,7 +127,7 @@ echo "********************************************************************"
echo "demux - FASTQ and SAM"
export PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test/dorado/test_demux.sh &> demux.log || die "test failed. See demux.log for details"
echo ""
echo "********************************************************************"
Expand Down Expand Up @@ -164,7 +164,7 @@ echo "********************************************************************"
echo "remora"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast.cfg
test/dorado/test_remora.sh &> remora.log || die "test failed. See remora.log for details"
echo ""
echo "********************************************************************"
Expand All @@ -182,7 +182,7 @@ echo "********************************************************************"
echo "R10.4.1 DNA - FAST model - 500k reads"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test/dorado/test.sh &> dna_500k.log || die "test failed. See dna_500k.log for details"
echo ""
echo "********************************************************************"
Expand All @@ -192,7 +192,7 @@ export PATH_TO_IDENTITY=/install/biorand/bin/identityrna.sh
export REFIDX=/genome/gencode.v40.transcripts.fa
export PATH_TO_FAST5=/data/slow5-testdata/uhr_prom_rna002_subsubsample/fast5/
export PATH_TO_BLOW5=/data/data/slow5-testdata/uhr_prom_rna002_subsubsample/PRPN119035_reads_20k.blow5
export MODEL=rna_r9.4.1_70bps_fast_prom.cfg
export MODEL=rna_r9.4.1_70bps_fast.cfg
test/dorado/test.sh &> rna.log || die "test failed. See rna.log for details"


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2 changes: 1 addition & 1 deletion test/dorado/test_qscore_split.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_sub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
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2 changes: 1 addition & 1 deletion test/dorado/test_qscore_split2.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_sub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
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2 changes: 1 addition & 1 deletion test/dorado/test_remora.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_chr
test -z $BIS && BIS=/data/slow5-testdata/hg2_prom_lsk114_chr22/chr22_bi.tsv
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $REF && REF=/genome/hg38noAlt.fa
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
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2 changes: 1 addition & 1 deletion test/dorado/test_seqsum.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_sub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
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2 changes: 1 addition & 1 deletion test/guppy/test.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/NA12878_prom_subsub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/NA12878_prom_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r9.4.1_450bps_fast_prom.cfg
test -z $MODEL && MODEL=dna_r9.4.1_450bps_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
Expand Down
2 changes: 1 addition & 1 deletion test/guppy/test_demux.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test -z $BARCODE && BARCODE=SQK-NBD114-96
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
Expand Down
2 changes: 1 addition & 1 deletion test/guppy/test_demux_qscore_split.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test -z $BARCODE && BARCODE=SQK-NBD114-96
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
Expand Down
14 changes: 7 additions & 7 deletions test/guppy/test_extensive.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -50,23 +50,23 @@ export REFIDX=/genome/hg38noAlt.idx
echo "R9.4.1 DNA - FAST model - 20k reads"
export PATH_TO_FAST5=/data/slow5-testdata/NA12878_prom_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/NA12878_prom_subsubsample/reads.blow5
export MODEL=dna_r9.4.1_450bps_fast_prom.cfg
export MODEL=dna_r9.4.1_450bps_fast.cfg
test/guppy/test.sh &> r9_dna_fast.log || die "test failed. see r9_dna_fast.log for details"
echo ""
echo "********************************************************************"

echo "R10.4.1 DNA - HAC model - 20k reads - split qscore inbuilt"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test/guppy/test_qscore_split.sh &> r10_split1.log || die "test failed. see r10_split1.log for details"
echo ""
echo "********************************************************************"

echo "R10.4.1 DNA - FAST model - 20k reads - split qscore script"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test/guppy/test_qscore_split2.sh &> r10_split2.log || die "test failed. See r10_split2.log for details"
echo ""
echo "********************************************************************"
Expand Down Expand Up @@ -126,7 +126,7 @@ echo "********************************************************************"
echo "demux - FASTQ and SAM"
export PATH_TO_FAST5=/data/slow5-testdata/barcode_test/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/barcode_test/merged_rand.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test/guppy/test_demux.sh &> demux.log || die "test failed. See demux.log for details"
echo ""
echo "********************************************************************"
Expand Down Expand Up @@ -163,7 +163,7 @@ echo "********************************************************************"
echo "remora"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast.cfg
test/guppy/test_remora.sh &> remora.log || die "test failed. See remora.log for details"
echo ""
echo "********************************************************************"
Expand All @@ -181,7 +181,7 @@ echo "********************************************************************"
echo "R10.4.1 DNA - FAST model"
export PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/fast5/
export PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
export MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
export MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test/guppy/test.sh &> dna_500k.log || die "test failed. See dna_500k.log for details"
echo ""
echo "********************************************************************"
Expand All @@ -191,7 +191,7 @@ export PATH_TO_IDENTITY=/install/biorand/bin/identityrna.sh
export REFIDX=/genome/gencode.v40.transcripts.fa
export PATH_TO_FAST5=/data/slow5-testdata/uhr_prom_rna002_subsubsample/fast5/
export PATH_TO_BLOW5=/data/data/slow5-testdata/uhr_prom_rna002_subsubsample/PRPN119035_reads_20k.blow5
export MODEL=rna_r9.4.1_70bps_fast_prom.cfg
export MODEL=rna_r9.4.1_70bps_fast.cfg
test/guppy/test.sh &> rna.log || die "test failed. See rna.log for details"


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2 changes: 1 addition & 1 deletion test/guppy/test_qscore_split.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_sub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_hac.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
Expand Down
2 changes: 1 addition & 1 deletion test/guppy/test_qscore_split2.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_sub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
Expand Down
2 changes: 1 addition & 1 deletion test/guppy/test_remora.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_chr
test -z $BIS && BIS=/data/slow5-testdata/hg2_prom_lsk114_chr22/chr22_bi.tsv
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_modbases_5mc_cg_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $REF && REF=/genome/hg38noAlt.fa
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
Expand Down
2 changes: 1 addition & 1 deletion test/guppy/test_seqsum.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ test -z $PATH_TO_FAST5 && PATH_TO_FAST5=/data/slow5-testdata/hg2_prom_lsk114_sub
test -z $PATH_TO_BLOW5 && PATH_TO_BLOW5=/data/slow5-testdata/hg2_prom_lsk114_subsubsample/reads.blow5
test -z $PATH_TO_IDENTITY && PATH_TO_IDENTITY=/install/biorand/bin/identitydna.sh
test -z $PATH_TO_EEL_VENV && PATH_TO_EEL_VENV=./venv3/bin/activate
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast_prom.cfg
test -z $MODEL && MODEL=dna_r10.4.1_e8.2_400bps_fast.cfg
test -z $REFIDX && REFIDX=/genome/hg38noAlt.idx
test -z $GUPPY_OUT_TMP && GUPPY_OUT_TMP=ont-guppy-tmp
test -z $EEL_OUT_TMP && EEL_OUT_TMP=buttery_eel_tmp
Expand Down

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