-
Notifications
You must be signed in to change notification settings - Fork 443
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1470 from mblue9/fix-hisat2
Fix HISAT2 strandedness parameter
- Loading branch information
Showing
18 changed files
with
951 additions
and
560 deletions.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,148 +1,30 @@ | ||
| <?xml version="1.0"?> | ||
| <macros> | ||
| <xml name="single_paired_selector"> | ||
| <param name="paired_selector" type="select" label="Single end or paired reads?"> | ||
| <option value="paired">Paired reads</option> | ||
| <option value="single">Unpaired reads</option> | ||
| <xml name="paired_end_options"> | ||
|
|
||
| <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information" | ||
| help="'FR' means a read corresponds to a transcript. 'RF' means a read corresponds to the reverse complemented counterpart of a transcript. With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome."> | ||
| <option value="">Unstranded</option> | ||
| <option value="FR">Forward (FR)</option> | ||
| <option value="RF">Reverse (RF)</option> | ||
| </param> | ||
| </xml> | ||
| <xml name="paired_input_conditional" tokens="ftype"> | ||
| <conditional name="paired"> | ||
| <expand macro="single_paired_selector" /> | ||
| <when value="paired"> | ||
| <conditional name="collection" label="Data structure"> | ||
| <param name="collection_selector" type="select" label="Input is structured as" help="If a list of pairs is selected, HISAT2 will run in batch mode over each pair in the list, producing a list of output bam files"> | ||
| <option value="files">Individual files</option> | ||
| <option value="collection">Pair collection or list of pairs</option> | ||
| </param> | ||
| <when value="collection"> | ||
| <param name="reads" type="data_collection" collection_type="paired" format="@FTYPE@" label="Paired reads" /> | ||
| </when> | ||
| <when value="files"> | ||
| <param name="forward" type="data" format="@FTYPE@" label="Forward reads" /> | ||
| <param name="reverse" type="data" format="@FTYPE@" label="Reverse reads" /> | ||
| </when> | ||
| </conditional> | ||
| <expand macro="paired_end_conditional" /> | ||
| <expand macro="paired_end_output" /> | ||
| </when> | ||
| <when value="single"> | ||
| <param name="reads" type="data" format="@FTYPE@" label="Reads" /> | ||
| <param name="unaligned_file" argument="--un-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" /> | ||
| <param name="aligned_file" argument="--al-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" /> | ||
| </when> | ||
| </conditional> | ||
| </xml> | ||
| <xml name="paired_end_conditional"> | ||
| <conditional name="paired_end_options"> | ||
| <param name="paired_end_options_selector" type="select" label="Paired-end options"> | ||
|
|
||
| <conditional name="paired_options"> | ||
| <param name="paired_options_selector" type="select" label="Paired-end options" help="See "Alignment Options" section of Help below for information"> | ||
| <option value="defaults">Use default values</option> | ||
| <option value="advanced">Specify paired-end parameters</option> | ||
| </param> | ||
| <when value="defaults" /> | ||
| <when value="defaults"/> | ||
| <when value="advanced"> | ||
| <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" label="Disable alignments of individual mates" help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior" /> | ||
| <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" label="Disable alignments of individual mates" help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior" /> | ||
| <param name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reference strand of reference" help="If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" /> | ||
| <param name="fr_rf_ff" argument="--fr/--rf/--ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" | ||
| help="E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)"> | ||
| <option value="--fr" selected="True">--fr</option> | ||
| <option value="--rf">--rf</option> | ||
| <option value="--ff">--ff</option> | ||
| </param> | ||
| <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="By default, when `hisat2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default: False"/> | ||
| <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `hisat2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default: False"/> | ||
| </when> | ||
| </conditional> | ||
| </xml> | ||
| <xml name="paired_end_output"> | ||
| <param name="unaligned_file" argument="--un-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" /> | ||
| <param name="aligned_file" argument="--al-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" /> | ||
| </xml> | ||
| <token name="@paired_end_options@"> | ||
| #if str( $input_format.paired.unaligned_file ) == "true": | ||
| #if $compressed == "GZ": | ||
| --un-conc-gz '${output_unaligned_reads_l}' | ||
| #else if $compressed == "BZ2": | ||
| --un-conc-bz2 '${output_unaligned_reads_l}' | ||
| #else: | ||
| --un-conc '${output_unaligned_reads_l}' | ||
| #end if | ||
| #end if | ||
| #if str( $input_format.paired.aligned_file ) == "true": | ||
| #if $compressed == "GZ": | ||
| --al-conc-gz '${output_aligned_reads_l}' | ||
| #else if $compressed == "BZ2" | ||
| --al-conc-bz2 '${output_aligned_reads_l}' | ||
| #else: | ||
| --al-conc '${output_aligned_reads_l}' | ||
| #end if | ||
| #end if | ||
| #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': | ||
| ${input_format.paired.paired_end_options.no_mixed} | ||
| ${input_format.paired.paired_end_options.no_discordant} | ||
| #end if | ||
| </token> | ||
| <token name="@strandedness_parameters@"> | ||
| #if str($spliced_options.spliced_options_selector) == "advanced": | ||
| #if str($spliced_options.rna_strandness).strip() != '': | ||
| --rna-strandness $spliced_options.rna_strandness | ||
| #end if | ||
| #end if | ||
| </token> | ||
| <token name="@FASTQGZ_SETUP@"> | ||
| <![CDATA[ | ||
| #set compressed="False" | ||
| #if str($input_format.paired.paired_selector) == 'paired': | ||
| #if str($input_format.paired.collection.collection_selector) == 'collection': | ||
| #if $input_format.paired.collection.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"): | ||
| #set read1 = "input_f.fastq.gz" | ||
| #set compressed = "GZ" | ||
| #else if $input_format.paired.collection.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): | ||
| #set read1 = "input_f.fastq.bz2" | ||
| #set compressed = "BZ2" | ||
| #else: | ||
| #set read1 = "input_f.fastq" | ||
| #end if | ||
| ln -f -s '${input_format.paired.collection.reads.forward}' ${read1} && | ||
|
|
||
| #if $input_format.paired.collection.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): | ||
| #set read2 = "input_r.fastq.gz" | ||
| #set compressed = "GZ" | ||
| #else if $input_format.paired.collection.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): | ||
| #set read2 = "input_r.fastq.bz2" | ||
| #set compressed = "BZ2" | ||
| #else: | ||
| #set read2 = "input_r.fastq" | ||
| #end if | ||
| ln -f -s '${input_format.paired.collection.reads.reverse}' ${read2} && | ||
| #else: | ||
| #if $input_format.paired.collection.forward.is_of_type("fastq.gz", "fastqsanger.gz"): | ||
| #set read1 = "input_f.fastq.gz" | ||
| #set compressed = "GZ" | ||
| #else if $input_format.paired.collection.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): | ||
| #set read1 = "input_f.fastq.bz2" | ||
| #set compressed = "BZ2" | ||
| #else: | ||
| #set read1 = "input_f.fastq" | ||
| #end if | ||
| ln -f -s '${input_format.paired.collection.forward}' ${read1} && | ||
| #if $input_format.paired.collection.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): | ||
| #set read2 = "input_r.fastq.gz" | ||
| #set compressed = "GZ" | ||
| #else if $input_format.paired.collection.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): | ||
| #set read2 = "input_r.fastq.bz2" | ||
| #set compressed = "BZ2" | ||
| #else: | ||
| #set read2 = "input_r.fastq" | ||
| #end if | ||
| ln -f -s '${input_format.paired.collection.reverse}' ${read2} && | ||
| #end if | ||
| #else: | ||
| #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"): | ||
| #set read1 = "input_f.fastq.gz" | ||
| #set compressed = "GZ" | ||
| #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"): | ||
| #set read1 = "input_f.fastq.bz2" | ||
| #set compressed = "BZ2" | ||
| #else: | ||
| #set read1 = "input_f.fastq" | ||
| #end if | ||
| ln -s '${input_format.paired.reads}' ${read1} && | ||
| #end if | ||
| ]]> | ||
| </token> | ||
| </macros> | ||
| </xml> | ||
| </macros> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| phiX phiX PhiX ${__HERE__}/phiX |
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| >phiX174 | ||
| GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT | ||
| GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA | ||
| ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG | ||
| TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA | ||
| GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC | ||
| TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT | ||
| TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT | ||
| CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT | ||
| TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG | ||
| TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC | ||
| GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA | ||
| CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG | ||
| TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT | ||
| AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC | ||
| CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA | ||
| TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC | ||
| TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA | ||
| CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA | ||
| GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT | ||
| GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA | ||
| ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC | ||
| TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT | ||
| TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC | ||
| ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC | ||
| CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT | ||
| GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC | ||
| CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC | ||
| TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG | ||
| TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT | ||
| TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA | ||
| AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT | ||
| TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT | ||
| ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC | ||
| GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC | ||
| TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT | ||
| TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA | ||
| TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG | ||
| TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC | ||
| CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG | ||
| AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC | ||
| CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT | ||
| TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG | ||
| CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA | ||
| AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT | ||
| GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG | ||
| GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA | ||
| TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT | ||
| CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG | ||
| TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA | ||
| GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC | ||
| CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA | ||
| TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA | ||
| AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC | ||
| TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT | ||
| CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA | ||
| TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG | ||
| TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT | ||
| CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT | ||
| TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC | ||
| ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG | ||
| TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA | ||
| ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG | ||
| GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC | ||
| CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT | ||
| GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG | ||
| GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT | ||
| ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG | ||
| CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC | ||
| CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC | ||
| GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT | ||
| CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG | ||
| CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA | ||
| TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT | ||
| TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG | ||
| TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC | ||
| AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC | ||
| TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| HISAT2 summary stats: | ||
| Total reads: 10 | ||
| Aligned 0 time: 0 (0.00%) | ||
| Aligned 1 time: 10 (100.00%) | ||
| Aligned >1 times: 0 (0.00%) | ||
| Overall alignment rate: 100.00% |
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| <tables> | ||
| <!-- Locations of indexes in the HISAT mapper format --> | ||
| <table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False"> | ||
| <columns>value, dbkey, name, path</columns> | ||
| <file path="${__HERE__}/test-data/cached_locally/hisat2_indexes.loc" /> | ||
| </table> | ||
| </tables> |