diff --git a/test/dorado/test.sh b/test/dorado/test.sh index 294e0b0..26bd4ae 100755 --- a/test/dorado/test.sh +++ b/test/dorado/test.sh @@ -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 diff --git a/test/dorado/test_demux.sh b/test/dorado/test_demux.sh index 274edfa..e678c89 100755 --- a/test/dorado/test_demux.sh +++ b/test/dorado/test_demux.sh @@ -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 diff --git a/test/dorado/test_demux_qscore_split.sh b/test/dorado/test_demux_qscore_split.sh index 73abc6f..27b9d65 100755 --- a/test/dorado/test_demux_qscore_split.sh +++ b/test/dorado/test_demux_qscore_split.sh @@ -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 diff --git a/test/dorado/test_extensive.sh b/test/dorado/test_extensive.sh index ea71267..fbfbf81 100755 --- a/test/dorado/test_extensive.sh +++ b/test/dorado/test_extensive.sh @@ -51,7 +51,7 @@ 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 "********************************************************************" @@ -59,7 +59,7 @@ 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 "********************************************************************" @@ -67,7 +67,7 @@ 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 "********************************************************************" @@ -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 "********************************************************************" @@ -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 "********************************************************************" @@ -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 "********************************************************************" @@ -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" diff --git a/test/dorado/test_qscore_split.sh b/test/dorado/test_qscore_split.sh index 4956f9c..0645935 100755 --- a/test/dorado/test_qscore_split.sh +++ b/test/dorado/test_qscore_split.sh @@ -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 diff --git a/test/dorado/test_qscore_split2.sh b/test/dorado/test_qscore_split2.sh index 5bbd009..9ba8e4a 100755 --- a/test/dorado/test_qscore_split2.sh +++ b/test/dorado/test_qscore_split2.sh @@ -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 diff --git a/test/dorado/test_remora.sh b/test/dorado/test_remora.sh index 8ce4591..976c68a 100755 --- a/test/dorado/test_remora.sh +++ b/test/dorado/test_remora.sh @@ -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 diff --git a/test/dorado/test_seqsum.sh b/test/dorado/test_seqsum.sh index ec870de..cb54edd 100755 --- a/test/dorado/test_seqsum.sh +++ b/test/dorado/test_seqsum.sh @@ -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 diff --git a/test/guppy/test.sh b/test/guppy/test.sh index a379492..734aa96 100755 --- a/test/guppy/test.sh +++ b/test/guppy/test.sh @@ -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 diff --git a/test/guppy/test_demux.sh b/test/guppy/test_demux.sh index 634cd90..1759bb8 100755 --- a/test/guppy/test_demux.sh +++ b/test/guppy/test_demux.sh @@ -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 diff --git a/test/guppy/test_demux_qscore_split.sh b/test/guppy/test_demux_qscore_split.sh index 7067dd2..84cf525 100755 --- a/test/guppy/test_demux_qscore_split.sh +++ b/test/guppy/test_demux_qscore_split.sh @@ -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 diff --git a/test/guppy/test_extensive.sh b/test/guppy/test_extensive.sh index eae36ce..0e270a4 100755 --- a/test/guppy/test_extensive.sh +++ b/test/guppy/test_extensive.sh @@ -50,7 +50,7 @@ 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 "********************************************************************" @@ -58,7 +58,7 @@ 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 "********************************************************************" @@ -66,7 +66,7 @@ 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 "********************************************************************" @@ -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 "********************************************************************" @@ -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 "********************************************************************" @@ -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 "********************************************************************" @@ -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" diff --git a/test/guppy/test_qscore_split.sh b/test/guppy/test_qscore_split.sh index aee0370..025089c 100755 --- a/test/guppy/test_qscore_split.sh +++ b/test/guppy/test_qscore_split.sh @@ -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 diff --git a/test/guppy/test_qscore_split2.sh b/test/guppy/test_qscore_split2.sh index 6aab1fb..e103c08 100755 --- a/test/guppy/test_qscore_split2.sh +++ b/test/guppy/test_qscore_split2.sh @@ -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 diff --git a/test/guppy/test_remora.sh b/test/guppy/test_remora.sh index 541f9e7..1ca55fb 100755 --- a/test/guppy/test_remora.sh +++ b/test/guppy/test_remora.sh @@ -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 diff --git a/test/guppy/test_seqsum.sh b/test/guppy/test_seqsum.sh index c6bbe0d..868d535 100755 --- a/test/guppy/test_seqsum.sh +++ b/test/guppy/test_seqsum.sh @@ -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