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Merge pull request #328 from LabKey/fb_merge_24.11_to_develop
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Merge discvr-24.11 to develop
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@bbimber
bbimber authored Dec 17, 2024
2 parents f0522c6 + 7f4cd5d commit ee787b2
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Showing 3 changed files with 81 additions and 19 deletions.
2 changes: 1 addition & 1 deletion SequenceAnalysis/pipeline_code/sequence_tools_install.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -617,7 +617,7 @@ then

mkdir blat
cd blat
wget $WGET_OPTS http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat
wget $WGET_OPTS https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat
chmod +x blat

install blat $LKTOOLS_DIR/blat
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19 changes: 13 additions & 6 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,9 @@ public ParagraphStep()
ToolParameterDescriptor.create("verbose", "Verbose Logging", "If checked, --verbose will be passed to paragraph to increase logging", "checkbox", new JSONObject(){{
put("checked", false);
}}, false),
ToolParameterDescriptor.create("useLocalScratch", "User local scratch", "If checked, the tool will write the intermediate temp files to a folder in the working directory, rather than the job's tempDir. This can make debugging easier.", "checkbox", new JSONObject(){{
put("checked", false);
}}, false),
ToolParameterDescriptor.create("retrieveReferenceSeq", "Retrieve Reference Sequence", "If checked, --debug will be passed to paragraph to increase logging", "checkbox", new JSONObject(){{
put("checked", false);
}}, false)
Expand Down Expand Up @@ -237,23 +240,27 @@ else if (!svVcf.exists())
paragraphArgs.add("-o");
paragraphArgs.add(paragraphOutDir.getPath());

File scratchDir = new File(ctx.getOutputDir(), "pgScratch");
if (scratchDir.exists())
File localScratchDir = new File(ctx.getOutputDir(), "pgScratch");
if (localScratchDir.exists())
{
try
{
FileUtils.deleteDirectory(scratchDir);
FileUtils.deleteDirectory(localScratchDir);
}
catch (IOException e)
{
throw new PipelineJobException(e);
}
}

paragraphArgs.add("--scratch-dir");
paragraphArgs.add(scratchDir.getPath());
boolean useLocalScratch = ctx.getParams().optBoolean("useLocalScratch", false);
if (useLocalScratch)
{
paragraphArgs.add("--scratch-dir");
paragraphArgs.add(localScratchDir.getPath());

ctx.getFileManager().addIntermediateFile(scratchDir);
ctx.getFileManager().addIntermediateFile(localScratchDir);
}

paragraphArgs.add("-i");
paragraphArgs.add(svVcf.getPath());
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79 changes: 67 additions & 12 deletions singlecell/resources/web/singlecell/panel/LibraryExportPanel.js
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
name: 'importType',
columns: 1,
items: [{
boxLabel: 'Novogene/Plate List',
boxLabel: '10x Plate List',
inputValue: 'plateList',
name: 'importType',
checked: true
Expand Down Expand Up @@ -112,7 +112,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
forceSelection: true,
editable: true,
allowBlank: true,
storeValues: ['Novogene', 'Novogene-New']
storeValues: ['Novogene', 'Novogene-New', 'MedGenome']
},{
xtype: 'textarea',
itemId: 'plateList',
Expand Down Expand Up @@ -145,7 +145,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
xtype: 'ldk-numberfield',
itemId: 'laneDataMax',
fieldLabel: 'Max Data Per Lane',
value: 700
value: 900
},{
xtype: 'ldk-numberfield',
itemId: 'defaultVolume',
Expand All @@ -167,26 +167,26 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
Ext4.Array.forEach(text, function(r, idx){
var val = r[0];
if (val.startsWith('G')){
val = val.substr(1);
val = val.substring(1);
val = val.replace('_', '-');
r[0] = 'GEX';
r.unshift(val);

}
else if (val.startsWith('T')){
val = val.substr(1);
val = val.substring(1);
val = val.replace('_', '-');
r[0] = 'VDJ';
r.unshift(val);
}
else if (val.startsWith('H') || val.startsWith('M')){
val = val.substr(1);
val = val.substring(1);
val = val.replace('_', '-');
r[0] = 'HTO';
r.unshift(val);
}
else if (val.startsWith('C')){
val = val.substr(1);
val = val.substring(1);
val = val.replace('_', '-');
r[0] = 'CITE';
r.unshift(val);
Expand All @@ -213,7 +213,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {

if (r[0].match('\\*$')) {
var m = r[0].match('\\*$');
var val = r[0].substr(0, m.index);
var val = r[0].substring(0, m.index);
wildcards[val] = r;
}
}, this);
Expand Down Expand Up @@ -843,7 +843,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
}, this);
}
}
else if (instrument === '10x Sample Sheet' || instrument === 'Novogene' || instrument === 'Novogene-New') {
else if (instrument === '10x Sample Sheet' || instrument === 'Novogene' || instrument === 'Novogene-New' || instrument === 'MedGenome') {
//we make the default assumption that we're using 10x primers, which are listed in the sample-sheet orientation
var doRC = false;
var rows = [];
Expand All @@ -862,7 +862,8 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {

var cleanedName = r[fieldName] + '_' + r[fieldName + '/name'].replace(/ /g, '_');
cleanedName = cleanedName.replace(/\//g, '-');
var sampleName = getSampleName(simpleSampleNames, r[fieldName], r[fieldName + '/name']) + (suffix && instrument.startsWith('Novogene') ? '' : '-' + suffix);
var sampleName = getSampleName(simpleSampleNames, r[fieldName], r[fieldName + '/name']) + (suffix && (instrument.startsWith('Novogene') || instrument === 'MedGenome') ? '' : '-' + suffix);
console.log(sampleName)

var barcode5s = r[fieldName + '/barcode5/sequence'] ? r[fieldName + '/barcode5/sequence'].split(',') : [];
if (!barcode5s.length) {
Expand Down Expand Up @@ -968,6 +969,53 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
data.push(r.laneAssignment || '');
data.push(barcode5Name || '');
}
else if (instrument === 'MedGenome') {
let libraryType = 'UNKNOWN';
switch (suffix) {
case 'GEX':
libraryType = '10x GEX';
break;
case 'TCR':
libraryType = '10X VDJ';
break;
case 'HTO':
libraryType = 'Cell Hashing';
case 'CITE':
libraryType = '10X Feature Barcode';
break;
default:
console.error('Unknown suffix: ' + suffix);
}

data = [sampleName];
data.push(r.plateAlias ? r.plateAlias : samplePrefix + r.plateId.replace(/-/g, '_'));
data.push(r.laneAssignment ? 'Pool on Lane ' + r.laneAssignment : '');
data.push('1.5 mL tube');
data.push(totalData + 'GB'); //Total data
data.push('PBMC'); // Source
data.push('Macaque'); // Species
data.push(libraryType);
data.push('10x'); // Kit type
data.push('10x'); // Index type

data.push(r[fieldName + '/barcode5']);
data.push(bc); // i7

data.push(r[fieldName + '/barcode3'])
data.push(bc3); //P5

data.push(size);

var quantity = defaultVolume * r[fieldName + '/concentration'];
data.push(quantity);
data.push(defaultVolume);
data.push(r[fieldName + '/concentration'] || '');

data.push(r.laneAssignment || '');
data.push(r.laneAssignment ? 'Lane ' + r.laneAssignment : '');

console.log(data)
}
rows.push(data.join(delim));
}, this);

Expand All @@ -978,7 +1026,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
}
};

var delim = instrument.startsWith('Novogene') ? '\t' : ',';
var delim = instrument.startsWith('Novogene') || instrument === 'MedGenome' ? '\t' : ',';
Ext4.Array.forEach(sortedRows, function (r) {
var totalCells = totalCellsByReadset[r.plateId];

Expand All @@ -994,7 +1042,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
}, this);

//add missing barcodes:
if (includeBlanks && !instrument.startsWith('Novogene')) {
if (includeBlanks && !instrument.startsWith('Novogene') && !instrument.startsWith('MedGenome')) {
var blankIdx = 0;
Ext4.Array.forEach(SingleCell.panel.LibraryExportPanel.TENX_BARCODES, function (barcode5) {
if (barcodeCombosUsed.indexOf(barcode5) === -1) {
Expand All @@ -1007,6 +1055,13 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
}
}, this);
}

if (instrument === 'MedGenome') {
console.log(rows)
Ext4.Array.forEach(rows, function(r, idx){
rows[idx] = (idx + 1) + '\t' + r;
}, this);
}
}

//check for unique barcodes
Expand Down

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