| Previous changeset 9:468b90c41cde (2023-06-21) Next changeset 11:93cfe7df7f8a (2025-02-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 20c6e3148d4adadc818754e77312cb11eb7af61e |
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modified:
artic_minion.xml macros.xml test-data/all_fasta.loc test-data/primer_scheme_bedfiles.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/clair3_models.loc test-data/gupplyplex_output1.fastq.gz test-data/gupplyplex_output2.fastq.gz test-data/primers.bed test-data/reference.fasta test-data/test.fastq.consensus.fasta test-data/test.fastq.gz test-data/test.merged.vcf.gz test-data/test.primertrimmed.rg.sorted.bam tool-data/models.loc.sample |
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removed:
test-data/SRR11410539_seqtk_sample_500_1.fastq test-data/SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta test-data/gupplyplex_output.fastq test-data/nCoV-2019.V1.bed test-data/nCoV-2019.reference.fasta test-data/nCoV-2019.scheme.V1.bed test-data/nCoV-2019.scheme.V3.bed test-data/test.fastq |
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| diff -r 468b90c41cde -r 02ea80c89fd1 artic_minion.xml --- a/artic_minion.xml Wed Jun 21 15:45:32 2023 +0000 +++ b/artic_minion.xml Fri Feb 21 22:12:51 2025 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="artic_minion" name="ARTIC minion" version="@PACKAGE_VERSION@+galaxy0" profile="20.09">\n+<tool id="artic_minion" name="ARTIC minion" version="@TOOL_VERSION@+galaxy0" profile="20.09">\n <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>\n <macros>\n <import>macros.xml</import>\n@@ -6,67 +6,112 @@\n <xrefs>\n <xref type="bio.tools">artic</xref>\n </xrefs>\n- <requirements>\n- <requirement type="package" version="@PACKAGE_VERSION@">artic</requirement>\n- </requirements>\n+ <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n- mkdir -p \'scheme/name/V1\' &&\n+\n+ #if $model_source.source == "built-in":\n+ ln -s \\$(dirname \\$(which run_clair3.sh))/models/$model_source.select_built_in clair3_model &&\n+ #else if $model_source.source == "datatable":\n+ #if $model_source.model.fields.source == "rerio" and $ont_license_agree != "true"\n+ echo "You must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement to use Rerio models." >&2 &&\n+ exit 2 ;\n+ #end if \n+ ln -s $model_source.model.fields.path clair3_model && \n+ #else if $model_source.source == "history":\n+ OUTNAME=`tar -tf $model_source.model | head -1 | cut -f1 -d"/"` &&\n+ tar -xf $model_source.model && \n+ mv \\$OUTNAME clair3_model &&\n+ #end if\n+\n #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":\n- ln -s \'${primer_scheme_source.primer_scheme_bedfile.fields.path}\' \'scheme/name/V1/name.scheme.bed\' &&\n+ ln -s \'${primer_scheme_source.bed.fields.path}\' \'primer.bed\' &&\n #else:\n- ln -s \'${primer_scheme_source.primer_scheme_bedfile}\' \'scheme/name/V1/name.scheme.bed\' &&\n+ ln -s \'${primer_scheme_source.bed}\' \'primer.bed\' &&\n #end if\n+\n #if str( $reference_source.reference_source_selector ) == "history":\n- ln -s \'${reference_source.reference}\' \'scheme/name/V1/name.reference.fasta\' &&\n- samtools faidx \'scheme/name/V1/name.reference.fasta\' &&\n+ ln -s \'${reference_source.reference}\' \'reference.fasta\' &&\n+ samtools faidx \'reference.fasta\' &&\n #else:\n- ln -s \'${reference_source.reference.fields.path}\' \'scheme/name/V1/name.reference.fasta\' &&\n- samtools faidx \'scheme/name/V1/name.reference.fasta\' &&\n+ ln -s \'${reference_source.reference.fields.path}\' \'reference.fasta\' &&\n+ samtools faidx \'reference.fasta\' &&\n #end if\n+\n artic minion\n+ --read-file \'${read_file}\'\n --threads \\${GALAXY_SLOTS:-1}\n+ --bed primer.bed\n+ --ref reference.fasta\n+ --model-dir .\n+ --model clair3_model\n+\n+ --min-depth $min_depth\n+ --min-mapq $min_mapq\n+ --primer-match-threshold $primer_match_threshold\n+ $align_consensus\n+\n #if $normalise > 0:\n --normalise ${normalise}\n #end if\n- --read-file \'${read_file}\'\n- --scheme-directory \'scheme\'\n- --medaka\n- --medaka-model \'$medaka_model\'\n- $bwa\n- \'name/V1\'\n- ## enclose the sample name in extra single quotes because\n- ## the minion pipeline script doesn\'t care about passing\n- ## its arguments safely.\n- "\'"\'${read_file.element_identifier}\'"\'"\n+\n+ ## enclose the sample name in extra single quotes because\n+ ## the minion pipeline script doesn\'t care about passing\n+ ## its arguments safely.\n+ "\'"\'${read_file.element_identifier}\'"\'"\n+ \n && bgzip -f \'${read_file.element_identifier}.fail.vcf\'\n ## remove enclosing single-quotes from header of output consensus fasta\n '..b'nformatics protocols; for example the `MPXV protocol`_.\n+\n+As of v1.5.1 Medaka is no longer used due to issues with long indels and has been replaced with `clair3`_ as the variant caller.\n+\n+ONT provides models for some latest or specific chemistries and basecallers through `Rerio`_. \n+\n+.. class:: warningmark\n+\n+**Please note:** By using these models you agree to ONT licensing which you `can read here`_.\n+\n+**Where to find amplicon schemes?**\n \n-This tool is configured to use the experimental \'medaka\' variant caller and must be supplied with the name of\n-a model file to use with \'medaka\', see the `medaka web page`_ for details.\n+The central location for publically available amplicon schemes is the `primalscheme website`_.\n+\n+Download the "primer.bed" and "reference.fasta" for input into this tool.\n+\n+**Amplicon Scheme Settings**\n \n-.. _ARTIC: https://artic.readthedocs.io/en/latest/\n-.. _medaka web page: https://github.com/nanoporetech/medaka#models\n+Each amplicon scheme will require slightly different minimum and maximum read length settings. On the `primalscheme website`_, under "Scheme Details" look for the \'ampliconsize\' value. Set the maximum value to the ampliconsize+100. If you are using the rapid kit, set the minimum to 200. For ligation kits, set the minimum read length to ampliconsize-200. For example, if the ampliconsize is 2500, maximum=2600, minimum(for ligation)=2300.\n+\n+**Which clair3 model to choose?**\n+\n+Model information is encoded in the fastq headers. In Galaxy, click on the `Display` (\xf0\x9f\x91\x81) icon, then inspect the end of the header file. For example: \n+\n+- Older software version would show only the model: `dna_r.9.4.1_minion_384`\n+- New version would provide all the required information: `basecall_model_version_id=dna_r10.4.1_e8.2_400bps_hac@v4.3.0`\n \n-Note that you should choose an appropriate model for the medaka version used by ARTIC minion.\n+See the documentation on how to read model names https://github.com/nanoporetech/dorado/?tab=readme-ov-file#decoding-dorado-model-names\n+\n+The three most important segments are:\n+\n+- Pore type - Flowcell chemistry - usually r1041 (R10) or r941 (R9). \n+- Model type - Model speed/accuracy - fast, hac or sup. \n+- Model version - eg v4.3.0 is equivalent to v430. \n+\n+Choose the model that is closest to your data.\n+\n+**Downloading Models**\n \n-================== ==================\n- ARTIC version medaka version\n-================== ==================\n- 1.2.1 1.0.3\n- 1.3.0-dev 1.2.3\n-================== ==================\n+First check with your Galaxy admins if preloaded Clair3 models are available. Or select \'Data Table\' under models to see if any are cached on your server. Only if required, you can download available models from the Rerio repository: https://github.com/nanoporetech/rerio. Please note: By using these models you agree to ONT licensing which you `can read here`_\n+\n+**Advanced pipeline parameters**\n+For majority of users the default parameter values will result in a good consensus sequence. You may wish to tweak the following parameters:\n+\n+- minimum mapping quality: The minimap2 mapping quality (phred) of reads against the specified reference.\n+- normalise: Increase this value to include more reads in the consensus generation step. This is per amplicon per strand, a value of a 100 would equate to an effective depth of 200. \n+- primer match threshold: When matching a read to a primer site, the pipeline allows for some deviation from the primer location. This value represents the max nucleotide distance between primer site and alignment position.\n+\n+.. _MPXV protocol: https://artic.network/mpxv/mpxv-bioinformatics-sop.html \n+.. _clair3: https://github.com/HKU-BAL/Clair3\n+.. _Rerio: https://github.com/nanoporetech/rerio\n+.. _can read here: https://raw.githubusercontent.com/nanoporetech/rerio/refs/heads/master/LICENCE.txt\n+.. _primalscheme website: labs.primalscheme.com\n ]]></help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r 468b90c41cde -r 02ea80c89fd1 macros.xml --- a/macros.xml Wed Jun 21 15:45:32 2023 +0000 +++ b/macros.xml Fri Feb 21 22:12:51 2025 +0000 |
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| @@ -1,12 +1,19 @@ <macros> - <token name="@PACKAGE_VERSION@">1.2.3</token> + <token name="@TOOL_VERSION@">1.6.0</token> <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">artic</requirement> + </requirements> + </xml> + <xml name="citations"> <citations> <citation type="bibtex"> @misc{githubartic-ncov2019, - author = {Nick Loman and the ZiBRA Project and the ARTIC project}, - year = {2017}, + author = {@Sam Wilkinson, Nick Loman and the ZiBRA Project and the ARTIC project}, + year = {2025}, title = {ARTIC toolkit}, publisher = {GitHub}, journal = {GitHub repository}, |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/SRR11410539_seqtk_sample_500_1.fastq --- a/test-data/SRR11410539_seqtk_sample_500_1.fastq Wed Jun 21 15:45:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2000 +0,0 @@\n-@SRR11410539.882919 882919/1\n-CTTGGGCATTAGTCGTTCAGTTACATGTACTAAGGTTAAACAGACGACTACAAACGGAATCCCGACAGCACCTACCAATAACTTTCAAATCGTAGTCTGTTCTCTAAATATGAACTTTAAAATCTGTGTGGCTGTCATCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCATCTTCTGCAGGCTGCTTACGGTTCGTCCGTGTTGCAGCCGATCCTCTTTATCTAGGTTTGTCGGGTGTGACCGAAGGTAAGATGGAGAGCCTTGTCCCCTGGTTTCAACGAGAAAACACGTCCAGTTTGCCTGTTTTACAGGTTCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGAGTCTTATCAGAGCACGTCAACATCTTAAAGATGAGGGTGCTATTGGTTTTCCCGTTTGTAGTCGTCTGTTTAACCTTAGCAATACGTAACTTT\n-+\n-$0%#%$##\'*(&)&&*)0/09711$$$&&/3%%)*3;:<:99:;;992&6;DF;<$&,2%%6/8:64=D@B?>:37//.11%%%%\'#%--($&%&)077AB:6A4/0.)\'(+.223301344/3%\'(*0169<,(3%\'\'$%%,+5//,((,40=,8%$8@>?=/&&15676.0++)1335:<:?<;>9;>=A??6**5<830-%&)4//265/1\'59:H@=>3//8:53/-13AE8<A:<:9:?977#%\'\'&&++.0&&)%$%&\'*12/05;ABC<4F)/AAAA?=99450*>;;=?B??B@/)+42.28122+*2/4//)<126,,.2,<9:,83$$-&9@<=6;<DA<<H4@@=CCAA3038)%%\'74.30+(/++*,.3010-7@A7<@C895.\'0:>@>54800+8=<70/6)*>9;EJBDE@0:24&\'(4<::3)).,.,/1,&,&*,0C=@<=9?;7>>;77*+,)-),%&*//;>B?<72&\'+*\n-@SRR11410539.1188960 1188960/1\n-TATTACTACCATTCGTTCCCATGCCTTACTAAGGTCACTCGACCAACTCTGGCATGAATCGACAGCACGCGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAGCTTTTGGCAATCATCTGGATGCACCCACACCACTAGGCATTGATTTAGATAGTGGAGTATGGCTACATACTACTTGTTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTTTACCCTCAGATGAGGATGAAGAAGGTGATTGTGAAGAGAAGTTTGAGCCATCAAACTCAATATGAGTATGTAGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCGCACTTCTGCATCTTCAACTGAAGAGCAAGAAGAAGATTGGTTAGATCGAAGGTGCTGTCAATTCCGTTTGTAGTAATCTGTTTAACCTTAGCAATACGTAACTT\n-+\n-#$#$$#$$%%%%\'%&$$%)(%%###$%($%))(\'(\'%"$%#$#%#%"\'-$"##$&%&*&086)%421$$*%&).6./8<ACFELGBBCACC>;:B@>D2:BF@21&+/?@C=80.B<<B?:<:9=<614)9844<?BABF93;11234\'/003+&\'*()%#&.9+)+)0%%(***/1632.&&&13>=><1./15-101\'*914,6=;?<=>:-.52261+((*\'-065280,-.;-58@32?EDA8923<0:552:8;602<;03+.<:=:?3/0(1>?<(780@/4)<?=2\'&8,,((2.)\'\'+-,&$5,+$&\'\'-22111<;4-:9:09-7((.-)&*,10%%$%*.&%167B@@EIFMD=79./40459::BA@=*/*0058&&,$$%029;:76\'$#//=9://1(++69;36=:\'0-,3)4//558=>--.%&&&-).<0.5&))&($\'%5499<+&+$$%%.64<9;?970((+</89994@:;00%%(\n-@SRR11410539.1794060 1794060/1\n-CATTTATTGCTTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACGGAATCGACAGCACCTAGCAGCATCTACAGCAAAAGCACAGAAAGATAATACAGTTGAATTGGCAGGCACTTCTGTTTGCATTACCAGCTTGTGAACGATGCTGTGGCAGCTAAACTACCAAGTACCATACCTCTATTTAGGTTGTTTTAATCCTTTAATAAAGTATAAATACTTCACTTTAGGACCTTTAGGTGTGTCTGTAACAAACCTACAAGGTGGTTTGATTCTGTATAGATAGTACCAGTTCCATCACTCTTAGGGAATCTGGCCATTTCAAATCATTAAATCGGATAACAGGCACAAGTACAAACCTACCTCCCTTTTGTTGTGTTGTAGTAAGCTAACGCATTGTCATCAGTGCAAGCAGTTTGTGTAGTACCGGCAGCACAAAGACATCTGTCGTAAGGTGCTGTCGATTCCGTTTAATAGTCGTCTGTTTAACCTTAGCAATACGTAACT\n-+\n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n-@SRR11410539.635976 635976/1\n-GTTGTACTTCGTTCGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACAGATCGACAGCACCTCATGGCTGCATCACGGTCAAATTCAGATTGCCACATTCAAGACTTCTTCAACTTTTTAAGAACAACCAGAATCACCATTAGCAACAGCCTGCTCATAAGCTTCTTGAGCAGTAGCAAAAACTGCATATGATGGAAGGGAACTAAACTCTGAGGCTATAGCTTGTAAGGTTGCCCTGTTGTCCAGCATTTCTTCACAAAGCTTGTTTATGTCTACAGCACCCTGCATGGAAAGCAAAACAGAAAGTAGTGAAACCATTTTTCAGGCTTCAGTAGTATCTTTAGCTAAGGAATGTCATTGTGTAACTGGACACATTGAGCCCACAATTTAGATGATGATTCTACTCTGAGTTGTTGCAAAACTGAGAGTAAGACTACTGATGTGCAAGGTGCTGTCGATTCCGTTGTAGTCGTCTGTTTAACCTTAGCAATACGTAAC\n-+\n-*$%)35;=@;=H<,*1)9?@EI>I=@?\'(5>IHEG93/3/6.+&%#$.269--<9=8:56168==FD>?,232,&%\'*.2056<9:8:2+%1+2/\'25:?@@:8-.--"#&/26F<?DVTSNB,,(9B?9)$*?767;AD@?99=9<>>?BI>B?A?A8C43/1&()+9HGDD89784447?>>9\'3\'+DB@CADB?;=,4,;A;A>?;<-?=<9<-4:4:>3-/&&)*8893>GF;93+8>67@))@B;C>?AC@C04,,-.\'$$$0:>@CB;@>BC?@>GFEHI@;68:44546>?=AAHI@55=5=><34>@A:==@@>B'..b'CGCCTCCTCCATGTTTAAGGTAAACATTGGCTGCATTAACAACCACTGTTGGTTTTACCTTTTAGCTTCTTCCATAATGTCTGCATTTTTAATGTATACATTGTCAGTAAGTTTTTAAATAACCACTAAAACTATTCACTTCAATAGTCTGAATAACTGGTAGTTCCATCTCTAATTGAGGTTGAACCTCAACAATTATTGAATAGTAGTTGCATCTGATTGTCCTCTGCCGTCTTGTTGACCAACAGTTTGTTGACTATCATCATCTAACCAATCTTCTTCTTGCTCTTCTTCAGGTTGAGCGAAGTGGCACAATTAGGTGCTGTCGGTCCGTTTGTAGTCGTCCTGTTTAACCTTGGCAATACGTAAC\n-+\n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n-@SRR11410539.817445 817445/1\n-CATTGTACTTCGTTCAGTTACGTATTGCTGGGTTAAACGGGCGACTACAAACAAGTCGACACAGCACCGCCCGGTTGAGTGTTGTCAATGCCAGATACGTGCTAAGCATATATTACGGTAACGACCCTGCTGCGCATCAGTTACCTCTTTGCTGTTGCTAGCTAAAGGACACACTGGAACCAGAATATTTCAGTTCGGTGTGAACTTATGAAAACTATGATCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATGTTGACACTGTAGCGTGCTTTGGTTTATGATAATAAACAACACATAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAGAGGTGCTGTCGATTCCGTTTGCCGGTCATCTGTTTAACCTTAGCAATACATAAC\n-+\n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n-@SRR11410539.1565287 1565287/1\n-CGGTATGCTTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACTACAAACGGAATCGACACTTCCTTCCCATCTGGTAAAGTTGAGGTTTGTATGGTACAAGTAACTTGTGGTACAACTACGCTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCTTAGGACAGACTTTTTCAGTGTTAACTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTAGGTGCTGTCGGTCCGTTTTGACGGCTCGTCTGTTTAACCTTAGCAATACGTAAC\n-+\n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n-@SRR11410539.1083900 1083900/1\n-GTTATTCGTTCAGTTACGTATTGCTAAGGTTAAACAGACGACCCCCTATAACAGATCGACAGCACCTCGTGAAATTGGGCCTCATAGCACGTGTATTAAACACCAGATGGTGAACCATTGTAACAAGCTAACTAGAAAATCTGTCCTGGTTGATTACGAACAAACTTATACTTGGAATTTGTGTTAGGTTGGCTGTATCAACCTTAAGCTTAAGTACAATTTTGCATAGAATGTCCAATAACCCTGAGTTGAACATTACCAGCCTGTACCAAGAAATTATGATTAGACTTACGAATGAGTAAATCTTCATAATTAGGGTTAAGCATGTCTTCAGAGTGCAGATCACATGTCTTGGACAGTAGCTTCCTGATGTCATCAAGCCAAAGACCGTTGGTGTAGTTTGTACCACAAGTTACTTGTACCATACAACCCTCAACTTTACCAGATGGGAAGGTGCAATGATTCGTTTGTAGTCGTCTGTTTAACTTATACTTAATACATATT\n-+\n-(%&##%*/;1+\')/3279::;>62<89/@=;12,)%)$/\'&(%%%#&%%\'\'+),79::B3/57531$&&110,++)-15889?735)/0+$(%$&#%&(/8.,-2/:9682:/@4:=DDAGEA=22((/+*%%&#&&&%7989++.2,.9.*%%%$%%%)2./)%%%/))&\'(&)#$$%&&&#.+)\'6+/49/.,52/;896:9:7985585768-BCEAGOJ>@<=>=:@5567?&\'#//5:B8;1?3@?==>====?;HDE<D>2-7:2.+35767(899KB=??;TI<==<A<89>;:<@=?IB7BAFGGFFECC=:/0*\';72-*(\')$$%*)%,443/4-2\'$+78A>?@>+&$(+%$$%%)&)\'\'&*51+<::7D@FG9,;;96<6#\'+,+)8.5=(%%786>>>::0)278<52??..8;321\'#(5269:<405<>9A<27<4;+0+%&&&&%%*.%%$4<94063-,0)@;;<=\'\'&,-(%%$$$))%#$%#$%\'\n' |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta --- a/test-data/SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta Wed Jun 21 15:45:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,500 +0,0 @@\n->SRR11410539_seqtk_sample_500_1.fastq/ARTIC/medaka 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|
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/all_fasta.loc --- a/test-data/all_fasta.loc Wed Jun 21 15:45:32 2023 +0000 +++ b/test-data/all_fasta.loc Fri Feb 21 22:12:51 2025 +0000 |
| b |
| @@ -4,4 +4,4 @@ # - name (Galaxy shows this in the UI) # - path (the reference file) # -test_entry test "Test Reference" ${__HERE__}/nCoV-2019.reference.fasta +test_fasta test "Test Reference" ${__HERE__}/reference.fasta |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/clair3_models.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clair3_models.loc Fri Feb 21 22:12:51 2025 +0000 |
| b |
| @@ -0,0 +1,10 @@ +#This file lists the names and locations of all the clair3 model files +#under the "clair3_models" directory (a directory that contains a directory +#for each build). This file has the format (white space characters are +#TAB characters): +# +#<unique_name> <platform> <sha256sum> <file_path> <source> +# +#So, clair3_models.loc could look something like this: +test_model ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 clair3 +r1041_e82_400bps_sup_v500 r1041_e82_400bps_sup_v500 ont 01c05768661bdd7de611e6bae1043c43b7523a54b223e029c683bfac0db7a678 /no/such/model rerio |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/gupplyplex_output.fastq --- a/test-data/gupplyplex_output.fastq Wed Jun 21 15:45:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,32 +0,0 @@ -@9bd6c9e7-e630-471b-88f5-f0f46e5b3767 -CATCGGTGTTGGCCCGTTTCAGTTACGTAACCTACCAACCAGCTTTCGATCTCTTGTAGATCTATTCTCTAAACGAACTTTAAAATCTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAGTACTGTCGTCTGACAGGACGAAATAACTCGTCTATCTTCTGCAGGCTGTTACGGTTTTCGTCCGTGTACGGCCGATCATCAACACATCTAGGTTTGTCCGGGTGTGACGAAAATGAATGGAAGCCTTGTCCCCTGGTTTCAACGAGAAAACACGTCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCATGCGTGGCTTTGGAACTCCGTGGAGGTCTTATCAGGGCATCAGCATGTAAAGATGAGCAATACGTAACT -+ -'%*+%%&#$%%%((*,88):*-++*,'$$#$%$#++13/*(%$$&/7%'13)034)--2/,7'$798<@8:<D568;@BDCLG216A88#)-;6..1%##''))++$$--)*+&(.,,.>>A2/0//1124664;67:>6014*8315---&'%%%%%%.+$%%)*%'''(*.%''37A8I<87*.,/552)$&%%$&=AB>9200402)&%'&)454?;>--8+'),)/8B/0C:=HB1((>&+030DE,6'01**))'+&&'''.0,020//4.&0(*7?A0/.023(2.42-+.(%=1.;:A3'A:)976;.LLP*%(,%2@=61.0&,,4/?D=&&&)(...$$,7)-,'<<B57///+,4888@344&(&'$$.?2*./(%)//01<''%5;;:<<=6231%% -@2912dba0-4acb-4b30-aa79-115c7c6e3c6c -CGATGTACTTCGTTCAGTTACGTAACACTACCAACCAACTTTCGATCTACCCGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCCGGCTGCATCGCCCAGTGCACTCACCAAGTATAATTAATAACTAATTACTGTCGTTGACAGGTTTTCGAGTAACTCTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTTACGACCGATCATCAACATCTATGATGGTTTTGTCAGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCCCTGGTTTCAGCGGAAAACTTTTACGTCAACTCAGTTTGCCTGTTTTACAGGTTGCGGCGATAACTCCCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGCACGTCAACATCATAAAGATGGCAATACGTAACTT -+ -$%'()+-552),54=(&$($((&&#$##&$'*-153./579958713%$%%%$%++2074@HBB674:;D889;BDC>FD=84:3(2(5/>BB0)B)(4?;*-781/-&'$###*+3++)1>B(&&))&,,-.-(00&2?=;>HE@C:/1.&(9E@70%%--%%%%&%./8;:993&.')4544)%(')*8?B?@F=898<LKKD:12831/99($"$##$).01)*0))'6;=;3+0&%).:KLG.'>&//;1$.98:1..,*==><6B87:8<<A55..%&&',**6&'8>:<++)+,,))%,,,+%$##&832::>1@ED.1>?@>EC3'%%$&1.-)&&',+,---**:2+(0+,%&#'()*-',002>=A/0<:>2%%-)*22269<B7%$8665==D62430,$&;;>?C??.<=<>>A<55+&'' -@80de96c0-f65f-45b6-9962-0646f207ffb2 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| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/gupplyplex_output1.fastq.gz |
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| Binary file test-data/gupplyplex_output1.fastq.gz has changed |
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| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/gupplyplex_output2.fastq.gz |
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| Binary file test-data/gupplyplex_output2.fastq.gz has changed |
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| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/nCoV-2019.V1.bed --- a/test-data/nCoV-2019.V1.bed Wed Jun 21 15:45:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/nCoV-2019.reference.fasta --- a/test-data/nCoV-2019.reference.fasta Wed Jun 21 15:45:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,500 +0,0 @@\n->MN908947.3\n-ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT\n-GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT\n-CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC\n-TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT\n-CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC\n-ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG\n-AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG\n-CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA\n-ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT\n-CGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGG\n-CGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGG\n-TGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGA\n-TCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGA\n-ACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG\n-CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTC\n-ATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCG\n-TGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCA\n-GACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAA\n-TTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAA\n-GCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATG\n-CAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA\n-GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGA\n-AGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGC\n-ATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGG\n-CTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTC\n-TTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGG\n-TTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGA\n-AATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA\n-GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAA\n-AGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTAC\n-AAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCC\n-TCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCT\n-TGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGG\n-AATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTAC\n-TAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG\n-GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGA\n-AGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTAT\n-CTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAA\n-GGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTC\n-TATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCA\n-CTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCC\n-TCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n-AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGA\n-AGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGA\n-AATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATAC\n-CTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGA\n-AGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGT\n-ACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGC\n-CTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC\n-ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGG\n-TGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGA\n-AGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGA\n-AGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGA\n-AGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGA\n-CGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATT\n-AGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT\n-AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGT\n-AAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGC\n-AGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGC\n-TACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAA\n-ACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAA\n-GAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGG\n-TATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA\n-TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGA\n'..b'ACTCA\n-ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATT\n-GTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTT\n-AATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAA\n-GCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTA\n-ATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCC\n-ATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTA\n-AAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT\n-CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAG\n-CCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAAT\n-GGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATG\n-CCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAG\n-TAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAA\n-TTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT\n-TCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC\n-TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAA\n-TCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTG\n-ACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACA\n-AATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACA\n-GGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGC\n-TTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAG\n-ATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA\n-AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGAT\n-GAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTG\n-ATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTA\n-CTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTA\n-GCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGAC\n-GGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGA\n-CAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n-ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACT\n-TCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTT\n-GGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAAT\n-TTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTAC\n-AGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATT\n-CTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGG\n-ATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT\n-GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTT\n-CGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAA\n-CGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTAC\n-GTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCG\n-ATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCT\n-CACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACAC\n-CAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG\n-TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGG\n-GCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGA\n-GGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGC\n-AATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAG\n-CAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAA\n-TTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGA\n-TGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG\n-TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAA\n-GAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAG\n-ACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAAC\n-TGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGG\n-AATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGC\n-CATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCA\n-TATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC\n-TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCC\n-TGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTC\n-AACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGC\n-TTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGC\n-ACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTA\n-GGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGT\n-ACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT\n-TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAA\n-AAAAAAAAAAAAAAAAAAAAAAA\n' |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/nCoV-2019.scheme.V1.bed --- a/test-data/nCoV-2019.scheme.V1.bed Wed Jun 21 15:45:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/primer_scheme_bedfiles.loc --- a/test-data/primer_scheme_bedfiles.loc Wed Jun 21 15:45:32 2023 +0000 +++ b/test-data/primer_scheme_bedfiles.loc Fri Feb 21 22:12:51 2025 +0000 |
| b |
| @@ -3,4 +3,4 @@ # - name (Galaxy shows this in the UI) # - path (the primer scheme bedfile) # -test_entry "Test Database" ${__HERE__}/nCoV-2019.scheme.V1.bed +test_bed "Test Bed" ${__HERE__}/primers.bed |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/primers.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers.bed Fri Feb 21 22:12:51 2025 +0000 |
| b |
| @@ -0,0 +1,58 @@ +MN908947.3 45 73 SARS-CoV-2_1_LEFT 1 + ATCTCTTGTAGATCTGTTCTCTAAACGA +MN908947.3 1157 1185 SARS-CoV-2_1_RIGHT 1 - GCAACTGGATAGACAGATCGAATTCTAC +MN908947.3 1073 1103 SARS-CoV-2_2_LEFT 2 + GTCCAAATTTTGTATTTCCCTTAAATTCCA +MN908947.3 2185 2213 SARS-CoV-2_2_RIGHT 2 - TAACAATTTCCCAACCGTCTCTAAGAAA +MN908947.3 2105 2135 SARS-CoV-2_3_LEFT 1 + CTAACATCTTTGGCACTGTTTATGAAAAAC +MN908947.3 3226 3246 SARS-CoV-2_3_RIGHT 1 - CTGCCGTCTTGTTGACCAAC +MN908947.3 3154 3176 SARS-CoV-2_4_LEFT 2 + GCCACTTCTGCTGCTCTTCAAC +MN908947.3 4270 4294 SARS-CoV-2_4_RIGHT 2 - CTTTGCCTCCTCTACAGTGTAACC +MN908947.3 4187 4211 SARS-CoV-2_5_LEFT 1 + GCACTACTGAAATGCTAGCGAAAG +MN908947.3 5299 5327 SARS-CoV-2_5_RIGHT 1 - ACTCTATTTGTTGGAGTGTTAACAATGC +MN908947.3 5198 5229 SARS-CoV-2_6_LEFT 2 + GGTACATGTCAGCATTAAATCACACTAAAAA +MN908947.3 6329 6356 SARS-CoV-2_6_RIGHT 2 - CTGACTTCAGTACATCAAACGAATTTG +MN908947.3 6250 6279 SARS-CoV-2_7_LEFT 1 + AATGCAACTAATAAAGCCACGTATAAACC +MN908947.3 7357 7390 SARS-CoV-2_7_RIGHT 1 - GGCCATTTGTACAAGATTAATTATTAACCACAT +MN908947.3 7282 7306 SARS-CoV-2_8_LEFT 2 + GTACTTGGATTGGCTGCAATCATG +MN908947.3 8393 8423 SARS-CoV-2_8_RIGHT 2 - ACATGAAATCTTTAACGTTCCATATCAAAG +MN908947.3 8320 8343 SARS-CoV-2_9_LEFT 1 + CGTGACCTTGGTGCTTGTATTGA +MN908947.3 9430 9460 SARS-CoV-2_9_RIGHT 1 - CATAAAATAGTAGGCAAGGCATGTTACTAC +MN908947.3 9347 9380 SARS-CoV-2_10_LEFT 2 + CTAATATGTTTACACCACTAATTCAACCTATTG +MN908947.3 10461 10488 SARS-CoV-2_10_RIGHT 2 - CATGAACCATTAAGGAATGAACCCTTA +MN908947.3 10381 10411 SARS-CoV-2_11_LEFT 1 + CAGACTTTTTCAGTGTTAGCTTGTTACAAT +MN908947.3 11474 11507 SARS-CoV-2_11_RIGHT 1 - CTACACCTGAGTAGTTAGAAGTAACAGAGATTA +MN908947.3 11390 11417 SARS-CoV-2_12_LEFT 2 + GGACACTTATGAATGTCTTGACACTCG +MN908947.3 12498 12530 SARS-CoV-2_12_RIGHT 2 - ATGTTGTACCATCACACGTATTTTTATATGTG +MN908947.3 12419 12444 SARS-CoV-2_13_LEFT 1 + CAAGAGATGGTTGTGTTCCCTTGAA +MN908947.3 13530 13559 SARS-CoV-2_13_RIGHT 1 - TCATTGTAGATGTCAAAAGCCCTGTATAC +MN908947.3 13458 13480 SARS-CoV-2_14_LEFT 2 + GTTTTTAAACGGGTTTGCGGTG +MN908947.3 14579 14599 SARS-CoV-2_14_RIGHT 2 - GATTACCAGAAGCAGCGTGC +MN908947.3 14491 14524 SARS-CoV-2_15_LEFT 1 + TAGGTGTTGTACATAATCAGGATGTAAACTTAC +MN908947.3 15601 15631 SARS-CoV-2_15_RIGHT 1 - GACACTCATAAAGTCTGTGTTGTAAATTGC +MN908947.3 15531 15551 SARS-CoV-2_16_LEFT 2 + CAAGCTGTCACGGCCAATGT +MN908947.3 16646 16671 SARS-CoV-2_16_RIGHT 2 - AAATGTCTCCTCAGTAGCTTTGAGC +MN908947.3 16571 16596 SARS-CoV-2_17_LEFT 1 + TGACTGGACAAATGCTGGTGATTAC +MN908947.3 17686 17711 SARS-CoV-2_17_RIGHT 1 - TGTGGCCTGTTAATTGCAGATGAAA +MN908947.3 17595 17627 SARS-CoV-2_18_LEFT 2 + GCTTTGGTTTATGATAATAAGCTTAAAGCACA +MN908947.3 18712 18737 SARS-CoV-2_18_RIGHT 2 - AATCCAATAGAATGATGCCAACAGG +MN908947.3 18636 18658 SARS-CoV-2_19_LEFT 1 + AAAATAGGACCTGAGCGCACCT +MN908947.3 19762 19790 SARS-CoV-2_19_RIGHT 1 - AGCTCAAATGCTACATTAACAGGTAATG +MN908947.3 19679 19712 SARS-CoV-2_20_LEFT 2 + TGAAGTACCAGTTTCTATCATTAATAACACTGT +MN908947.3 20787 20819 SARS-CoV-2_20_RIGHT 2 - AAATATTGACACAGTTGAGTATATTTTGCGAC +MN908947.3 20682 20711 SARS-CoV-2_21_LEFT 1 + GTTGCTATGCCTAATCTTTACAAAATGCA +MN908947.3 21801 21828 SARS-CoV-2_21_RIGHT 1 - CCATCATTAAATGGTAGGACAGGGTTA +MN908947.3 21695 21723 SARS-CoV-2_22_LEFT 2 + CCTCAGTTTTACATTCAACTCAGGACTT +MN908947.3 22825 22858 SARS-CoV-2_22_RIGHT 2 - GCAGCCTGTAAAATCATCTGGTAATTTATAATT +MN908947.3 22742 22774 SARS-CoV-2_23_LEFT 1 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT +MN908947.3 23868 23895 SARS-CoV-2_23_RIGHT 1 - GTGTTTTTGTCTTGTTCAACAGCTATT +MN908947.3 23784 23811 SARS-CoV-2_24_LEFT 2 + CATTTGTGGTGATTCAACTGAATGCAG +MN908947.3 24875 24905 SARS-CoV-2_24_RIGHT 2 - TGATTTGTGGTTCATAAAAATTCCTTTGTG +MN908947.3 24797 24822 SARS-CoV-2_25_LEFT 1 + CTGCCATTTGTCATGATGGAAAAGC +MN908947.3 25911 25937 SARS-CoV-2_25_RIGHT 1 - TGTTCAGAAATAGGACTTGTTGTGCC +MN908947.3 25784 25809 SARS-CoV-2_26_LEFT 2 + GAAATGCCGTTCCAAAAACCCATTA +MN908947.3 26899 26924 SARS-CoV-2_26_RIGHT 2 - TAGAAGCGGTCTGGTCAGAATAGTG +MN908947.3 26818 26840 SARS-CoV-2_27_LEFT 1 + TTTCAGACTGTTTGCGCGTACG +MN908947.3 27934 27962 SARS-CoV-2_27_RIGHT 1 - CTGTAAACTACATTCTTGGTGAAATGCA +MN908947.3 27832 27860 SARS-CoV-2_28_LEFT 2 + TATCTTTTGGTTCTCACTTGAACTGCAA +MN908947.3 28945 28969 SARS-CoV-2_28_RIGHT 2 - GCTCTCAAGCTGGTTCAATCTGTC +MN908947.3 28702 28723 SARS-CoV-2_29_LEFT 1 + GATCACATTGGCACCCGCAAT +MN908947.3 29779 29802 SARS-CoV-2_29_RIGHT 1 - GGCTCTTCCATATAGGCAGCTCT |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/reference.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fasta Fri Feb 21 22:12:51 2025 +0000 |
| b |
| b'@@ -0,0 +1,429 @@\n+>MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome\n+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA\n+CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC\n+TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG\n+TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC\n+CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC\n+GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG\n+CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT\n+GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC\n+GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT\n+TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA\n+GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG\n+TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG\n+CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG\n+TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG\n+CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA\n+ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA\n+CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC\n+CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA\n+GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT\n+ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG\n+GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG\n+CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA\n+CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA\n+ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA\n+GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT\n+TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG\n+GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG\n+TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC\n+GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG\n+ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG\n+GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT\n+AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA\n+TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT\n+AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA\n+GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC\n+TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n+AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA\n+GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT\n+ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA\n+GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT\n+GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA\n+ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC\n+ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA\n+TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG\n+AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT\n+TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA\n+CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC\n+AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT\n+AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA\n+GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA\n+CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG\n+TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT\n+GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT\n+TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCAC'..b'CAGACTATTACCAGCTGTACTCA\n+ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC\n+CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT\n+TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC\n+TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT\n+TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT\n+GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT\n+CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA\n+TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC\n+CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA\n+AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT\n+AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC\n+ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC\n+TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT\n+GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA\n+GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG\n+ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG\n+CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC\n+TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA\n+AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC\n+CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA\n+GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA\n+TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT\n+TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT\n+GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n+ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG\n+CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA\n+GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG\n+TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC\n+GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA\n+TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT\n+GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA\n+AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG\n+ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG\n+TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT\n+GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC\n+CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG\n+TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT\n+GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA\n+AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC\n+ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT\n+AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA\n+ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG\n+TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG\n+CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC\n+AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA\n+ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG\n+TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC\n+TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC\n+TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT\n+TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG\n+CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT\n+GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT\n+TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC\n+GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT\n+TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAA\n' |
| b |
| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/test.fastq --- a/test-data/test.fastq Wed Jun 21 15:45:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b"@@ -1,40 +0,0 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| b'@@ -0,0 +1,500 @@\n+>test.fastq.gz/MN908947.3/ARTIC/clair3 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| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/test.fastq.gz |
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| Binary file test-data/test.fastq.gz has changed |
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| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/test.merged.vcf.gz |
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| Binary file test-data/test.merged.vcf.gz has changed |
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| diff -r 468b90c41cde -r 02ea80c89fd1 test-data/test.primertrimmed.rg.sorted.bam |
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| Binary file test-data/test.primertrimmed.rg.sorted.bam has changed |
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| diff -r 468b90c41cde -r 02ea80c89fd1 tool-data/models.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/models.loc.sample Fri Feb 21 22:12:51 2025 +0000 |
| b |
| @@ -0,0 +1,18 @@ +#Enter the model names in the second column, the platform name in the second and the path in the third. +#This file lists the locations and dbkeys of all the model files +#under the "models" directory (a directory that contains a directory +#for each build). This file has the format (white space characters are +#TAB characters): +# +#<id> <name> <platform> <path> +# +#So, all_model.loc could look something like this: +test_model "the_model_name" r941_prom_hac_g360+g422 $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422#This file lists the names and locations of all the clair3 model files +#under the "clair3_models" directory (a directory that contains a directory +#for each build). This file has the format (white space characters are +#TAB characters): +# +#<unique_name> <platform> <sha256sum> <file_path> <source> +# +#So, clair3_models.loc could look something like this: +test_model ont $(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422 clair3 |
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| diff -r 468b90c41cde -r 02ea80c89fd1 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Jun 21 15:45:32 2023 +0000 +++ b/tool_data_table_conf.xml.sample Fri Feb 21 22:12:51 2025 +0000 |
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| @@ -10,4 +10,8 @@ <columns>value, dbkey, name, path</columns> <file path="tool-data/all_fasta.loc" /> </table> + <table name="model" comment_char="#"> + <columns>value, platform, sha256, path, source</columns> + <file path="tool-data/model.loc" /> + </table> </tables> |
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| diff -r 468b90c41cde -r 02ea80c89fd1 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Wed Jun 21 15:45:32 2023 +0000 +++ b/tool_data_table_conf.xml.test Fri Feb 21 22:12:51 2025 +0000 |
| b |
| @@ -9,4 +9,8 @@ <columns>value, dbkey, name, path</columns> <file path="${__HERE__}/test-data/all_fasta.loc" /> </table> + <table name="model" comment_char="#"> + <columns>value, platform, sha256, path, source</columns> + <file path="${__HERE__}/test-data/clair3_models.loc" /> + </table> </tables> |