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Merge pull request #5160 from gallardoalba/Update_STARSOLO
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Update STARSOLO: add Velocyto option
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@bgruening
bgruening authored Mar 9, 2023
2 parents 2948f11 + 8b78274 commit f6ccf9e
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Showing 2 changed files with 70 additions and 5 deletions.
2 changes: 1 addition & 1 deletion tools/rgrnastar/macros.xml
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the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
<!-- STAR version to be used -->
<token name="@TOOL_VERSION@">2.7.10b</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@PROFILE@">21.01</token>
<!-- STAR index version compatible with this version of STAR
This is the STAR version that introduced the index structure expected
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73 changes: 69 additions & 4 deletions tools/rgrnastar/rg_rnaStarSolo.xml
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--soloOutFormatFeaturesGeneField3 '${solo.soloOutFormatFeaturesGeneField3}'
## Unmapped
'$solo.outSAMunmapped'
$solo.outSAMunmapped
## Read MAPQ
--outSAMmapqUnique ${solo.outSAMmapqUnique}
## Limits
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##outWig:
@OUTWIG@
## Rename the the selected features directory
&& mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures
#if $solo.soloFeatures == 'Gene Velocyto'
&& mv Solo.out/Velocyto Solo.out/soloFeatures
#else
&& mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures
#end if
## put the barcodes and features stats into a single file
&& cat <(echo "Barcodes:") Solo.out/Barcodes.stats <(echo "Genes:") Solo.out/soloFeatures/Features.stats > '${output_stats}'
#if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != 'None':
## recompress BAM output for smaller file size
&& samtools view -b -o '$output_BAM' Aligned.sortedByCoord.out.bam
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#end if
##outWig:
@OUTWIGOUTPUTS@
]]></command>
<configfiles>
<configfile name="manifest_file" >
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<option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option>
<option value="GeneFull_ExonOverIntron" >Full: Count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons</option>
<option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option>
<option value="Gene Velocyto">Velocyto: calculate spliced, unspliced, and ambiguous counts per cell per gene similar to the velocyto tool</option>
</param>
<conditional name="filter" >
<param name="filter_type" type="select" label="Cell filtering type and parameters" >
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</assert_contents>
</output>
</test>
<test expect_num_outputs="6">
<!-- test 12 -->
<conditional name="refGenomeSource">
<param name="geneSource" value="history" />
<param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
<param name="genomeSAindexNbases" value="4" />
<param name="sjdbOverhang" value="100" />
<param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>
</conditional>
<conditional name="sc" >
<param name="solo_type" value="CB_UMI_Simple" />
<conditional name="input_types">
<param name="use" value="repeat" />
<param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
<param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
</conditional>
<param name="soloCBwhitelist" value="filtered.barcodes.txt" />
<conditional name="params">
<param name="chemistry" value="Cv3" />
</conditional>
<conditional name="umidedup">
<param name="soloUMIdedup" value="1MM_All" />
</conditional>
</conditional>
<section name="solo" >
<conditional name="filter">
<param name="filter_type" value="no_filter" />
</conditional>
<param name="soloStrand" value="Forward" />
<param name="soloFeatures" value="Gene Velocyto" />
<param name="quantModeGene" value="true" />
</section>
<output name="output_barcodes" >
<assert_contents>
<!-- first and last line -->
<has_line line="AAACCTGAGCGCTCCA" />
<has_line line="TTTGGTTAGTGGGCTA" />
<has_n_lines n="394" />
</assert_contents>
</output>
<output name="output_genes">
<assert_contents>
<has_line_matching expression="ENSG00000279493\s+FP565260\.4\s+Gene\s+Expression" />
<has_line_matching expression="ENSG00000279064\s+FP236315\.1\s+Gene\s+Expression" />
<has_n_lines n="14" />
</assert_contents>
</output>
<output name="output_stats" >
<assert_contents>
<has_line_matching expression="\s+noUnmapped\s+0" />
<has_line_matching expression="\s+yesUMIs\s+36" />
</assert_contents>
</output>
<output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
<output name="reads_per_gene" >
<assert_contents>
<has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />
<has_line_matching expression="ENSG00000275464\s+38\s+1\s+40" />
</assert_contents>
<metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
</output>
</test>
</tests>
<help><![CDATA[
**What it does**
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