updated raw analysis

app/raw_analysis/CELLRANGER_MULTI_template_v1.txt

@@ -0,0 +1,46 @@
+sample_metadata:
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+    feature_types: Gene Expression/Antibody Capture/CRISPR Guide Capture/Multiplexing Capture/VDJ-B/VDJ-T/VDJ-T-GD/Antigen Capture
+    cellranger_group: GROUP_NAME
+analysis_metadata:
+  cellranger_multi_config:
+    - "[gene-expression]"
+    - "reference,/project/tgu/resources/pipeline_resource/transcriptome/cellranger/v7/GRCh38/refdata-gex-GRCh38-2020-A"
+    - "# probe-set,/path/to/probe/set, # Required, Fixed RNA Profiling only."
+    - "# filter-probes,<true|false>, # Optional, Fixed RNA Profiling only."
+    - "# r1-length,<int>"
+    - "# r2-length,<int>"
+    - "# chemistry,<auto>"
+    - "# expect-cells,<int>"
+    - "# force-cells,<int>"
+    - "# no-secondary,<true|false>"
+    - "# no-bam,<true|false>"
+    - "# check-library-compatibility,<true|false>"
+    - "# include-introns,<true|false>"
+    - "# min-assignment-confidence,<0.9>, # Optional, Cell Multiplexing only."
+    - "# cmo-set,/path/to/CMO/reference, # Optional, Cell Multiplexing only."
+    - "# barcode-sample-assignment,/path/to/barcode-sample-assignment/csv, # Optional, Cell Multiplexing only."
+    - "[feature] # For Feature Barcode libraries only"
+    - "# reference,/path/to/feature/reference"
+    - "# r1-length,<int>"
+    - "# r2-length,<int>"
+    - "# [vdj] # For TCR and BCR libraries only"
+    - "reference,/project/tgu/resources/pipeline_resource/vdj/v7/hg38/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0"
+    - "# inner-enrichment-primers,/path/to/primers"
+    - "# r1-length,<int>"
+    - "# r2-length,<int>"
+    - "[antigen-specificity] # for 5' BCR/TCR Antigen Capture only"
+    - "#control_id,mhc_allele"
+    - "#[samples] # for Cell Multiplexing libraries only"
+    - "#sample_id,cmo_ids,description"
+    - "#[samples] # for Fixed RNA Profiling multiplexed libraries only"
+    - "#sample_id,probe_barcode_ids,description"
+  scanpy:
+    MITO_PREFIX: MT-
+    RUN_SCRUBLET: true
+    RUN_CELLCYCLE_SCORE: true
+    CELL_MARKER_LIST: /project/tgu/resources/pipeline_resource/cell_markers/PangaloDB/PanglaoDB_markers_27_Mar_2020.tsv
+    CELL_MARKER_SPECIES: HG38
+    S_GENES: ''
+    G2M_GENES: ''
+    CELL_MARKER_MODE: NON-VDJ

app/raw_analysis/GEOMX_DCC.txt

@@ -1,9 +1,9 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}:
-        dsp_id: 
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+  dsp_id: 
 {% endfor -%}
 analysis_metadata:
-    config_zip_file: /rds/general/project/genomics-facility-archive-2019/live/orwell/GeoMx/
-    geomx_pkc_file: /rds/general/project/genomics-facility-archive-2019/live/orwell/GeoMx/GeoMx_PKC_Files/Hs_R_NGS_WTA_v1.0.pkc
-    geomx_dcc_params:
-        - "--threads=8"
+  config_zip_file: /rds/general/project/genomics-facility-archive-2019/live/orwell/GeoMx/
+  geomx_pkc_file: /rds/general/project/genomics-facility-archive-2019/live/orwell/GeoMx/GeoMx_PKC_Files/Hs_R_NGS_WTA_v1.0.pkc
+  geomx_dcc_params:
+    - "--threads=8"

app/raw_analysis/NF_ATAC_template_v1.txt

@@ -1,11 +1,11 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}:
-        sample: SAMPLE_NAME
-        replicate: REPLICATE_ID
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+    sample: SAMPLE_NAME
+    replicate: REPLICATE_ID
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/atacseq
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/atacseq
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/NF_Ampliseq_template_v1.txt

@@ -1,10 +1,10 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}:
-        condition: CONDITION_NAME
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+  condition: CONDITION_NAME
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/ampliseq
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/ampliseq
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/NF_Bactmap_template_v1.txt

@@ -1,9 +1,9 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}: ""
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}: ""
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/bactmap
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/bactmap
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/NF_ChIP_template_v1.txt

@@ -1,11 +1,11 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}:
-        antibody: ANTIBODY_NAME
-        control: CONTROL_SAMPLE_ID
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+    antibody: ANTIBODY_NAME
+    control: CONTROL_SAMPLE_ID
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/chipseq
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/chipseq
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/NF_CutAndRun_template_v1.txt

@@ -1,12 +1,12 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}:
-        group: GROUP_NAME
-        replicate: REPLICATE_ID
-        control: CONTROL_SAMPLE_ID
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+    group: GROUP_NAME
+    replicate: REPLICATE_ID
+    control: CONTROL_SAMPLE_ID
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/cutandrun
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/cutandrun
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/NF_HIC_template_v1.txt

@@ -1,9 +1,9 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}: ""
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}: ""
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/hic
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/hic
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/NF_Methylseq_template_v1.txt

@@ -1,10 +1,10 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}: ""
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}: ""
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/methylseq
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
-        - "--aligner bismark"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/methylseq
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"
+    - "--aligner bismark"

app/raw_analysis/NF_RNA_template_v1.txt

@@ -1,13 +1,13 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}:
-        condition: CONDITION_NAME (USE CAPS)
-        strandedness: reverse
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+  condition: CONDITION_NAME (USE CAPS)
+  strandedness: reverse
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/rnaseq
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
-        - "--aligner star_rsem"
-        - "--seq_center IGF"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/rnaseq
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"
+    - "--aligner star_rsem"
+    - "--seq_center IGF"

app/raw_analysis/NF_Sarek_template_v1.txt

@@ -1,12 +1,12 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}:
-        patient: PATIENT_ID
-        sex: SEX
-        status: STATUS_ID
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}:
+  patient: PATIENT_ID
+  sex: SEX
+  status: STATUS_ID
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/sarek
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/sarek
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/NF_smRNA_template_v1.txt

@@ -1,9 +1,9 @@
 sample_metadata:
-{% for SAMPLE_ID in SAMPLE_ID_LIST %}    {{ SAMPLE_ID }}: ""
+{% for SAMPLE_ID in SAMPLE_ID_LIST %}  {{ SAMPLE_ID }}: ""
 {% endfor -%}
 analysis_metadata:
-    NXF_VER: X.Y.Z
-    nfcore_pipeline: nf-core/smrnaseq
-    nextflow_params:
-        - "-profile singularity"
-        - "-r A.B"
+  NXF_VER: X.Y.Z
+  nfcore_pipeline: nf-core/smrnaseq
+  nextflow_params:
+    - "-profile singularity"
+    - "-r A.B"

app/raw_analysis/analysis_validation_cellranger_multi_v1

@@ -0,0 +1,59 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "id": "https://github.com/imperial-genomics-facility/IGFPortal",
+    "title": "IGF Cellranger Multi analysis validation schema",
+    "description": "Schema for validation of Cellranger multi analysis yaml file",
+    "type" : "object",
+    "version": "0.0.1",
+    "properties": {
+        "sample_metadata": {
+            "type": "object",
+            "uniqueItems": true,
+            "minItems": 1,
+            "patternProperties": {
+                "^IGF[a-zA-Z0-9-_]+$": {
+                    "type": ["object", "string"],
+                    "properties": {
+                        "feature_types": {
+                            "type": "string",
+                            "enum": [
+                               "Gene Expression",
+                               "Antibody Capture",
+                               "CRISPR Guide Capture",
+                               "Multiplexing Capture",
+                               "VDJ-B",
+                               "VDJ-T",
+                               "VDJ-T-GD",
+                               "Antigen Capture"
+                            ]
+                        },
+                        "cellranger_group": {
+                            "type": "string",
+                            "pattern": "^[A-Z0-9-_]+$"
+                        }
+                    }
+                }
+            }
+        },
+        "analysis_metadata": {
+            "type": "object",
+            "properties": {
+                "scanpy": {
+                    "type": "object",
+                    "uniqueItems": true,
+                    "minItems": 1
+                },
+                "cellranger_multi_config": {
+                    "type": "array",
+                    "uniqueItems": true,
+                    "minItems": 1,
+                    "items": {
+                        "type": "string"
+                    }
+                }
+            },
+            "required": ["cellranger_multi_config", "scanpy"]
+        }
+    },
+    "required": ["sample_metadata", "analysis_metadata"]
+}

app/raw_analysis_view.py

@@ -223,21 +223,21 @@ class RawAnalysisView(ModelView):
     def reject_raw_analysis(self, item):
         try:
             if isinstance(item, list):
-                for i in item:
-                    try:
+                try:
+                    for i in item:
                         db.session.\
                             query(RawAnalysis).\
                             filter(RawAnalysis.raw_analysis_id==i.raw_analysis_id).\
                             update({'status': 'REJECTED'})
-                        db.session.commit()
-                    except:
-                        db.session.rollback()
-                        raise
+                    db.session.commit()
+                except:
+                    db.session.rollback()
+                    raise
             else:
                 try:
                     db.session.\
                         query(RawAnalysis).\
-                        filter(RawAnalysis.raw_analysis_id==i.raw_analysis_id).\
+                        filter(RawAnalysis.raw_analysis_id==item.raw_analysis_id).\
                         update({'status': 'REJECTED'})
                     db.session.commit()
                 except:
@@ -574,6 +574,28 @@ def template_geomx_dcc(self, item):
             log.error(e)
             return redirect(url_for('RawAnalysisView.list'))
 
+    @action("template_cellranger_multi", "Template cellranger multi", confirmation=None, icon="fa-file-excel-o", multiple=False, single=True)
+    def template_cellranger_multi(self, item):
+        try:
+            template_tag = "CELLRANGER_MULTI"
+            if item.project_id is not None:
+                formatted_template = \
+                    generate_analysis_template(
+                        project_igf_id=item.project.project_igf_id,
+                        template_tag=template_tag)
+                output = BytesIO(formatted_template.encode('utf-8'))
+                analysis_name = item.analysis_name.encode('utf-8').decode()
+                output.seek(0)
+                self.update_redirect()
+                return send_file(output, download_name=f"{analysis_name}_{template_tag}_analysis.yaml", as_attachment=True)
+            else:
+                flash(f"Failed to generate {template_tag} template, no project", 'danger')
+                return redirect(url_for('RawAnalysisView.list'))
+        except Exception as e:
+            flash(f"Failed to generate {template_tag} template", 'danger')
+            log.error(e)
+            return redirect(url_for('RawAnalysisView.list'))
+
 
 class RawAnalysisQueueView(ModelView):
     datamodel = SQLAInterface(RawAnalysis)