From 611b76ec2dca3ff79a3d5392c5bb3e46d4ddf47e Mon Sep 17 00:00:00 2001 From: Tom Harrop Date: Mon, 24 Jun 2024 12:13:20 +1000 Subject: [PATCH] models --- tools/dorado/README.md | 6 +- .../dorado/tool-data/dorado_models.loc.sample | 58 +++++++++++++++++++ 2 files changed, 62 insertions(+), 2 deletions(-) diff --git a/tools/dorado/README.md b/tools/dorado/README.md index cffee22b..218e90f9 100644 --- a/tools/dorado/README.md +++ b/tools/dorado/README.md @@ -40,7 +40,9 @@ apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \ The loc file doesn't have a header, so you can keep it sorted. ```bash -sort -t$'\t' -k1,1V tool-data/dorado_models.loc.sample \ - > tool-data/dorado_models.loc.sample +cp tool-data/dorado_models.loc.sample \ + tool-data/dorado_models.loc.sample.old && +sort -t$'\t' -k1,1V tool-data/dorado_models.loc.sample.old \ + > tool-data/dorado_models.loc ``` diff --git a/tools/dorado/tool-data/dorado_models.loc.sample b/tools/dorado/tool-data/dorado_models.loc.sample index e69de29b..e84d214e 100644 --- a/tools/dorado/tool-data/dorado_models.loc.sample +++ b/tools/dorado/tool-data/dorado_models.loc.sample @@ -0,0 +1,58 @@ +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_fast@v4.1.0 /models/dna_r10.4.1_e8.2_260bps_fast@v4.1.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_hac@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_hac@v4.1.0 /models/dna_r10.4.1_e8.2_260bps_hac@v4.1.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_sup@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_sup@v4.1.0 /models/dna_r10.4.1_e8.2_260bps_sup@v4.1.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_fast@v4.1.0 /models/dna_r10.4.1_e8.2_400bps_fast@v4.1.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.2.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_fast@v4.2.0 /models/dna_r10.4.1_e8.2_400bps_fast@v4.2.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v4.3.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_fast@v4.3.0 /models/dna_r10.4.1_e8.2_400bps_fast@v4.3.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_fast@v5.0.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_fast@v5.0.0 /models/dna_r10.4.1_e8.2_400bps_fast@v5.0.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v4.1.0 /models/dna_r10.4.1_e8.2_400bps_hac@v4.1.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v4.3.0 /models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1 /models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1 /models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2 /models/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v5.0.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v5.0.0 /models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1 /models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1 /models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1 /models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1 /models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v4.1.0 /models/dna_r10.4.1_e8.2_400bps_sup@v4.1.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v4.3.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v4.3.0 /models/dna_r10.4.1_e8.2_400bps_sup@v4.3.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1 /models/dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1 /models/dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2 /models/dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v5.0.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v5.0.0 /models/dna_r10.4.1_e8.2_400bps_sup@v5.0.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1 /models/dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1 /models/dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1 /models/dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1 /models/dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_5khz_stereo@v1.3 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_5khz_stereo@v1.3 /models/dna_r10.4.1_e8.2_5khz_stereo@v1.3 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_fast@v3.4 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_fast@v3.4 /models/dna_r9.4.1_e8_fast@v3.4 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1 /models/dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0 /models/dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_hac@v3.3 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_hac@v3.3 /models/dna_r9.4.1_e8_hac@v3.3 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1 /models/dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0 /models/dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_sup@v3.3 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_sup@v3.3 /models/dna_r9.4.1_e8_sup@v3.3 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1 /models/dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0 /models/dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r9.4.1_e8_sup@v3.6 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r9.4.1_e8_sup@v3.6 /models/dna_r9.4.1_e8_sup@v3.6 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna002_70bps_fast@v3 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna002_70bps_fast@v3 /models/rna002_70bps_fast@v3 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna002_70bps_hac@v3 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna002_70bps_hac@v3 /models/rna002_70bps_hac@v3 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_fast@v3.0.1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_fast@v3.0.1 /models/rna004_130bps_fast@v3.0.1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_fast@v5.0.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_fast@v5.0.0 /models/rna004_130bps_fast@v5.0.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_hac@v3.0.1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_hac@v3.0.1 /models/rna004_130bps_hac@v3.0.1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_hac@v5.0.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_hac@v5.0.0 /models/rna004_130bps_hac@v5.0.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_hac@v5.0.0_m6A@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_hac@v5.0.0_m6A@v1 /models/rna004_130bps_hac@v5.0.0_m6A@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_hac@v5.0.0_pseU@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_hac@v5.0.0_pseU@v1 /models/rna004_130bps_hac@v5.0.0_pseU@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_sup@v3.0.1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_sup@v3.0.1 /models/rna004_130bps_sup@v3.0.1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_sup@v3.0.1_m6A_DRACH@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_sup@v3.0.1_m6A_DRACH@v1 /models/rna004_130bps_sup@v3.0.1_m6A_DRACH@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_sup@v5.0.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_sup@v5.0.0 /models/rna004_130bps_sup@v5.0.0 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_sup@v5.0.0_m6A@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_sup@v5.0.0_m6A@v1 /models/rna004_130bps_sup@v5.0.0_m6A@v1 +1c65eb070a9fc1d88710c4dc09b06541f96fdd28_rna004_130bps_sup@v5.0.0_pseU@v1 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 rna004_130bps_sup@v5.0.0_pseU@v1 /models/rna004_130bps_sup@v5.0.0_pseU@v1