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new recipe names
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Updating LaunchMetrics and run_param_config to be able to handle new recipe names from sample sheet
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@darrelln32
darrelln32 committed May 21, 2024
1 parent d4c5e5b commit 49420eb
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Showing 2 changed files with 52 additions and 37 deletions.
6 changes: 3 additions & 3 deletions scripts/LaunchMetrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,9 @@
# Global Variable : we do not want to process these experiments in this script
DO_NOT_PROCESS = ["DLP"]
# These recipes will be evaluated using DRAGEN because of their larger size of fastqs
RUN_ON_DRAGEN = ["MissionBio", "SingleCellCNV", "MouseWholeGenome", "HumanWholeGenome", "PombeWholeGenome", "ChIPSeq", "AmpliconSeq"]
RUN_ON_DRAGEN = ["MissionBio", "SingleCellCNV", "WGS_Deep", "ChIP", "CUT&RUN","Amplicon"]
# these projects willl only need demux stats
DEMUX_ONLY = ["SMARTSeq", "10X_Genomics"]
DEMUX_ONLY = ["SMARTSeq", "Chromium", "10X_Genomics"]

# Organisms to have DRAGEN BAMS
DRAGEN_RNA_GENOMES = ["GRCh38", "grcm39"]
Expand Down Expand Up @@ -85,7 +85,7 @@ def launch_metrics(self, all_samples, run, project_directory):
self.dragen(sample, run, sample_parameters, work_directory, dragen_directory, fastq_list)
continue
# check for methylated samples
if ((sample.recipe == "MethylCaptureSeq") or (sample.recipe == "WholeGenomeBisulfiteSequencing")):
if ("Methyl" in sample.recipe):
pathlib.Path(dragen_directory).mkdir(parents = True, exist_ok = True)
self.dragen_methylation(sample, run, sample_parameters, work_directory, dragen_directory, fastq_list)
continue
Expand Down
83 changes: 49 additions & 34 deletions scripts/run_param_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,25 +59,25 @@ def get_ordered_dic(unordered_dic):
Returns:
type, OrderedDict: Ordered dictionary by key-length
"""
return OrderedDict(sorted(unordered_dic.items(), key=lambda t: -len(t[0])))
return OrderedDict(sorted(unordered_dic.items(), key = lambda t: -len(t[0])))

""" Mapping of recipes to their type, default should be DNA """
recipe_type_mapping_UNORDERED = {
"MouseWholeGenome": { TYPE: "WGS" },
"PigWholeGenome": { TYPE: "WGS" },
"PombeWholeGenome": { TYPE: "WGS" },
"ShallowWGS": { TYPE: "WGS" },
"10X_Genomics_WGS": { TYPE: "WGS" },
"WholeGenomeSequencing": { TYPE: "WGS" },
"HumanWholeGenome": { TYPE: "WGS" },
# "MouseWholeGenome": { TYPE: "WGS" },
# "PigWholeGenome": { TYPE: "WGS" },
# "PombeWholeGenome": { TYPE: "WGS" },
"WGS_Shallow": { TYPE: "WGS" },
# "10X_Genomics_WGS": { TYPE: "WGS" },
"WGS_Metagenomic": { TYPE: "WGS" },
"WGS_Deep": { TYPE: "WGS" },
".*RNA.*": { TYPE: "RNA" },
".*96Well_SmartSeq2": { TYPE: "RNA" },
# ".*96Well_SmartSeq2": { TYPE: "RNA" },
".*SMARTer.*": { TYPE: "RNA" },
"FusionDiscoverySeq": { TYPE: "RNA" },
# "FusionDiscoverySeq": { TYPE: "RNA" },
".*Ribo.*": { TYPE: "RNA" },
"SMART-Seq": { TYPE: "RNA" },
# "SMART-Seq": { TYPE: "RNA" },
"SMARTSeq": { TYPE: "RNA" },
".*CDH1_RNA.*": { TYPE: "CAPTURE" },
# ".*CDH1_RNA.*": { TYPE: "CAPTURE" },
# FOR NEW ENTRIES
# "{regex}": { TYPE: type }
".*": { TYPE: "DNA" } # DEFAULT
Expand All @@ -97,16 +97,16 @@ def get_ordered_dic(unordered_dic):
"RDM": "hg19",
"myTYPE_V1": "hg19",
"PanCancerV2": "hg19",
"MissionBio-Heme": "GRCh38",
"User_MissionBio": "GRCh38",
"WholeExome_v4": "hg19",
"AmpliSeq": "hg19",
"HemeBrainPACT_v1": "hg19"
},
"Mouse": {
"M-IMPACT_v1": "mm10",
"M-IMPACT_v2": "mm10",
"HC_IMPACT-Mouse": "mm10",
"Twist_mWES": "mm10",
"10X_Genomics_Multiome": "mm10"
"SC_Chromium-Multiome": "mm10"
}
}
""" Mapping of species to their genome-type """
Expand Down Expand Up @@ -432,7 +432,8 @@ def get_ordered_dic(unordered_dic):
MSKQ: "yes",
MD: "yes"
},
"IMPACT505": {
"HC_IMPACT": {
# IMPACT505
# NOTE: interval list file name "IMPACT468_BAITS" is stored in LIMS and passed to pipelines, change file name with caution
BAITS: "/igo/home/igo/resources/ilist/hg38/IMPACT505/IMPACT505_BAITS.baits",
TARGETS: "/igo/home/igo/resources/ilist/hg38/IMPACT505/IMPACT505_TARGETS.targets",
Expand All @@ -445,13 +446,15 @@ def get_ordered_dic(unordered_dic):
MSKQ: "yes",
MD: "yes"
},
"IMPACT-Heme": {
"HC_IMPACT-Heme": {
# IMPACT-Heme
BAITS: "/igo/home/igo/resources/ilist/hg38/IMPACT-Heme_v2/IMPACT-Heme_v2_BAITS.iList",
TARGETS: "/igo/home/igo/resources/ilist/hg38/IMPACT-Heme_v2/IMPACT-Heme_v2_TARGETS.iList",
MSKQ: "yes",
MD: "yes"
},
"IMPACT_Heme_v2": {
"HC_IMPACT-Heme": {
# IMPACT_Heme_v2
BAITS: "/igo/home/igo/resources/ilist/hg38/IMPACT-Heme_v2/IMPACT-Heme_v2_BAITS.iList",
TARGETS: "/igo/home/igo/resources/ilist/hg38/IMPACT-Heme_v2/IMPACT-Heme_v2_TARGETS.iList",
MSKQ: "yes",
Expand All @@ -463,7 +466,8 @@ def get_ordered_dic(unordered_dic):
MSKQ: "yes",
MD: "yes"
},
"M-IMPACT_v2": {
"HC_IMPACT-Mouse": {
# M-IMPACT_v2
BAITS: "/home/igo/resources/BED-Targets/IMPACT/MM_IMPACT/M-IMPACT_v2.baits",
TARGETS: "/home/igo/resources/BED-Targets/IMPACT/MM_IMPACT/M-IMPACT_v2.targets",
MSKQ: "yes",
Expand Down Expand Up @@ -501,10 +505,11 @@ def get_ordered_dic(unordered_dic):
MD: "yes"
},
"IDT_Exome_v2_FP_Viral_Probes": {
BAITS: "/igo/home/igo/resources/ilist/hg38/IDT_Exome_v2_FP/IDT_Exome_v2_FP_BAITS.baits",
TARGETS: "/igo/home/igo/resources/ilist/hg38/IDT_Exome_v2_FP/IDT_Exome_v2_FP_TARGETS.targets",
MSKQ: "no",
MD: "yes"
# IDT_Exome_v2_FP_Viral_Probes or WES_Human
BAITS: "/igo/home/igo/resources/ilist/hg38/IDT_Exome_v2_FP/IDT_Exome_v2_FP_BAITS.baits",
TARGETS: "/igo/home/igo/resources/ilist/hg38/IDT_Exome_v2_FP/IDT_Exome_v2_FP_TARGETS.targets",
MSKQ: "no",
MD: "yes"
},
"IDT_Exome_v1": {
BAITS: "/home/igo/resources/BED-Targets/xgen-exome-research-panel-BAITS.iList",
Expand Down Expand Up @@ -548,14 +553,16 @@ def get_ordered_dic(unordered_dic):
MSKQ: "yes",
MD: "yes"
},
"MSK-ACCESS_v1": {
"HC_ACCESS": {
# MSK-ACCESS_v1
BAITS: "/igo/home/igo/resources/ilist/hg38/MSK-ACCESS-v1/MSK-ACCESS-v1_0-probesAllwFP.baits",
TARGETS: "/igo/home/igo/resources/ilist/hg38/MSK-ACCESS-v1/MSK-ACCESS-v1_0-probesAllwFP.targets",
MSKQ: "no",
MD: "yes",
HAPLOTYPE_MAP: "/home/igo/fingerprint_maps/map_files/hg38_no_chr_ACCESS_unordered.map"
},
"MSK-ACCESS_v2": {
"HC_ACCESS": {
# MSK-ACCESS_v2
BAITS: "/igo/home/igo/resources/ilist/hg38/MSK-ACCESS-v2/MSK-ACCESS-v2_0-probesAllwFP.baits",
TARGETS: "/igo/home/igo/resources/ilist/hg38/MSK-ACCESS-v2/MSK-ACCESS-v2_0-probesAllwFP.targets",
MSKQ: "no",
Expand All @@ -574,7 +581,8 @@ def get_ordered_dic(unordered_dic):
MSKQ: "no",
MD: "yes"
},
"MissionBio-Heme": {
"User_MissionBio": {
# MissionBio-Heme
BAITS: "/igo/work/nabors/bed_files/Mission_Bio/hg38/MissionBio-Heme_BAITS.iList",
TARGETS: "/igo/work/nabors/bed_files/Mission_Bio/hg38/MissionBio-Heme_TARGETS.iList",
MSKQ: "no",
Expand Down Expand Up @@ -648,33 +656,38 @@ def get_ordered_dic(unordered_dic):
MSKQ: "no",
MD: "yes"
},
"MethylCaptureSeq": {
"Methyl_Capture": {
# MethylCaptureSeq
BAITS: "/igo/home/igo/resources/ilist/hg38/MethylCaptureSeq/truseq-methyl-capture-epic-manifest-file-hg38.baits.ilist",
TARGETS: "/igo/home/igo/resources/ilist/hg38/MethylCaptureSeq/truseq-methyl-capture-epic-manifest-file-hg38.targets.ilist",
MSKQ: "no",
MD: "yes"
},
"MSK-CH": {
"HC_CMOCH": {
# MSK-CH
BAITS: "/igo/home/igo/resources/ilist/hg38/CMO-CH/CMO-CH.hg38.baits",
TARGETS: "/igo/home/igo/resources/ilist/hg38/CMO-CH/CMO-CH.hg38.targets",
MSKQ: "no",
MD: "yes"
},
"CMO-CH": {
"HC_CMOCH": {
# CMO-CH
BAITS: "/igo/home/igo/resources/ilist/hg38/CMO-CH/CMO-CH.hg38.baits",
TARGETS: "/igo/home/igo/resources/ilist/hg38/CMO-CH/CMO-CH.hg38.targets",
MSKQ: "no",
MD: "yes"
},
"HumanWholeGenome": {
"WGS_Deep": {
# HumanWholeGenome
MSKQ: "no",
MD: "yes",
HAPLOTYPE_MAP: "", # TODO - Add this
GENOME: "/igo/work/genomes/H.sapiens/GRCh38.p13/ncbi-genomes-2021-09-23/GCF_000001405.39_GRCh38.p13_genomic.fna", # References that created DRAGEN reference
REFERENCE: "/igo/work/genomes/H.sapiens/GRCh38.p13/ncbi-genomes-2021-09-23/GCF_000001405.39_GRCh38.p13_genomic.fna",
DGN_REFERENCE: "/staging/ref/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559"
},
"MouseWholeGenome": {
"WGS_Deep": {
# MouseWholeGenome
MSKQ: "no",
MD: "yes"
# TODO
Expand All @@ -692,7 +705,7 @@ def get_ordered_dic(unordered_dic):
# TODO
# sh $DIR/../PicardScripts/LaunchPipelines.sh $RUNTYPE --input /igo/work/FASTQ/$RUNNAME/$PROJECT/ --genome $GENOME --type WGS --md $MARKDUPLICATES --mskq $MSKQ
},
"ShallowWGS": {
"WGS_Shallow": {
MSKQ: "no",
MD: "yes"
# TODO
Expand All @@ -710,13 +723,15 @@ def get_ordered_dic(unordered_dic):
# TODO
# sh $DIR/../PicardScripts/LaunchPipelines.sh $RUNTYPE --input /igo/work/FASTQ/$RUNNAME/$PROJECT/ --genome $GENOME --md $MARKDUPLICATES --mskq $MSKQ
},
"AmpliconSeq": {
"DNA_Amplicon": {
# AmpliconSeq
MSKQ: "no",
MD: "yes"
# TODO
# sh $DIR/../PicardScripts/LaunchPipelines.sh $RUNTYPE --input /igo/work/FASTQ/$RUNNAME/$PROJECT/ --genome $GENOME --md $MARKDUPLICATES --mskq $MSKQ
},
"CRISPRSeq": {
"DNA_CRISPR": {
# CRISPRSeq
MSKQ: "no",
MD: "yes"
# TODO
Expand Down

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