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Merged
bbimber merged 4 commits into from
Dec 17, 2024
Merged

Merge discvr-24.11 to develop #328

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b5990d7
Allow paragraph to write to normal scratch dir
bbimber Dec 13, 2024
d4ee1a5
Use HTTPS for download
bbimber Dec 13, 2024
020ff29
Support alternate sequence centers
bbimber Dec 13, 2024
7f4cd5d
Merge discvr-24.11 to develop
bbimber Dec 13, 2024
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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
Expand Down
19 changes: 13 additions & 6 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/ParagraphStep.java
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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());
Expand Down
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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