diff --git a/app/scripts/config/AnalysisConfig.js b/app/scripts/config/AnalysisConfig.js index 4585ec3..54525ff 100644 --- a/app/scripts/config/AnalysisConfig.js +++ b/app/scripts/config/AnalysisConfig.js @@ -91,7 +91,7 @@ var AnalysisConfig = { "vdjserver:activity:uses": { "JobFiles": [ 'archive' ], "SequenceFASTQ": [ 'sequence_reads', 'sequence_single_read', 'sequence_quality' ], - "SequenceFASTA": [ 'sequence_reads', 'sequence_single_read' ], + "SequenceFASTA": [ 'sequence_reads' ], "SequenceQualityFiles": [ 'sequence_quality'], "SequenceForwardPairedFiles": ['sequence_forward_paired_reads'], "SequenceReversePairedFiles": ['sequence_reverse_paired_reads'] , @@ -115,9 +115,9 @@ var AnalysisConfig = { "igblast": { "vdjserver:name":"IgBlast", "activity": { - "igblast-ls6-0.10": { + "igblast-ls6-0.11": { "vdjserver:app:name": "igblast-ls6", - "vdjserver:app:version": "0.10", + "vdjserver:app:version": "0.11", "vdjserver:app:default": true } }, diff --git a/app/scripts/models/AnalysisDocument.js b/app/scripts/models/AnalysisDocument.js index 835bcfe..1274afe 100644 --- a/app/scripts/models/AnalysisDocument.js +++ b/app/scripts/models/AnalysisDocument.js @@ -164,6 +164,25 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata) let use_type = app['vdjserver:activity:uses'][input_name][ut]; console.log(input_name, use_type); switch(use_type) { + case 'sequence_single_read': + for (let i in rep['sample']) { + let seqfiles = rep['sample'][i]['sequencing_files']; + //console.log(seqfiles); + if (seqfiles['filename'] && seqfiles['file_type'] == 'fastq') { + found = true; + new_entity_id.push('vdjserver:project_file:' + seqfiles['filename']); + let extra = {}; + extra[input_name] = seqfiles['filename']; + extra['airr:Repertoire'] = rep['repertoire_id'] + new_uses_id.push('vdjserver:app:inputs:' + activity_id + ':' + seqfiles['filename']); + if (project_file_map[seqfiles['filename']]) { + extra['vdjserver:uuid'] = project_file_map[seqfiles['filename']]; + } + extras.push(extra); + } + } + break; + case 'sequence_forward_paired_reads': // identifiers use the forward read file for (let i in rep['sample']) { @@ -225,7 +244,7 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata) case 'sequence': for (let i in rep['sample']) { let seqfiles = rep['sample'][i]['sequencing_files']; - console.log(seqfiles); + //console.log(seqfiles); if (seqfiles['filename'] && seqfiles['file_type'] == 'fasta') { found = true; new_entity_id.push('vdjserver:project_file:' + seqfiles['filename']); @@ -241,7 +260,6 @@ AnalysisDocument.prototype.expand_airr_types = async function(project_metadata) } break; - case 'sequence_single_read': case 'sequence_quality': case 'sequence_reads': case 'archive': diff --git a/app/vdjserver-schema b/app/vdjserver-schema index 5459c75..8bbce5f 160000 --- a/app/vdjserver-schema +++ b/app/vdjserver-schema @@ -1 +1 @@ -Subproject commit 5459c75e4498ffa35c4f227a6f7fceabc0774340 +Subproject commit 8bbce5f7fb0f79eca744ea9c47bd5c2298cf1988