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fix: add missing type
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@Smeds
Smeds committed Aug 24, 2023
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26 changes: 26 additions & 0 deletions config/references/design_files.hg19.yaml
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cnv_amp_genes:
path: cnv/cnv_amp_genes.bed
checksum: 7bae2d8c592e54207c4b8effaca2bf4f
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/cnv_amp_genes.bed

cnv_loh_genes:
path: cnv/cnv_loh_genes.bed
checksum: 38d3acbe99bb9626ccc0ab1815b6e35b
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/cnv_loh_genes.bed

bcftools_filter_include_region:
exon:
path: design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed
checksum: c85f3369444cd6f27a397eef0a24fff9
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.230222.bed

bcftools_filter_exclude_region:
blacklist:
checksum: 2eaeb99aa53fc2b7b173c328b6bd1672
path: cnv/cnvkit_germline_blacklist_20221221.bed
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/cnvkit_germline_blacklist_20221221.bed

bcftools_id_snps:
snps_bed:
checksum: ab9b7084d599606bb52142d26158f5e1
path: design/ID_SNPs.bed
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/ID_SNPs.bed

call_small_cnv_amplifications:
regions_file:
checksum: 24447a09e6691ca7382f4400b06943cf
path: cnv/cnv_amplification_genes.tsv
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/cnv_amplification_genes.tsv

call_small_cnv_deletions:
regions_file:
checksum: e044cf88e5e50e68a3a797be5720e6c0
path: cnv/cnv_deletion_genes.tsv
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/cnv_deletion_genes.tsv

exon_skipping:
design_bed:
checksum: 7fe64299477aa4b6a5f5783cce9fa30f
path: design/Twist_RNA_Design5.annotated.bed
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/Twist_RNA_Design5.annotated.bed

filter_fuseq_wes:
gene_white_list:
checksum: d762e65cc9d9d01d022db7de7c31cc68
path: fuseq_wes/fuseq_wes_gene_white_list.txt
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/fuseq_wes/fuseq_wes_gene_white_list.txt

transcript_black_list:
checksum: 586ad13ce609fdf5390d299cbbaae183
path: fuseq_wes/fuseq_wes_transcript_black_list.txt
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/fuseq_wes/fuseq_wes_transcript_black_list.txt

fuseq_wes:
params:
checksum: d2e6d449027c49e24f026261082fa5bb
path: fuseq_wes/fuseq_params.txt
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/fuseq_wes/fuseq_params.txt

gatk_collect_allelic_counts:
SNP_interval:
checksum: 47cee8e04769d13e1c282fedf7333eac
path: cnv/gnomad_SNP_0.001_target.annotated.interval_list
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/gnomad_SNP_0.001_target.annotated.interval_list

gene_fuse:
genes:
checksum: c35fc6fbf81ce2e1cc55b536742ccf02
path: gene_fuse/GMS560_fusion_w_pool2.hg19.221117.csv
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/gene_fuse/GMS560_fusion_w_pool2.hg19.221117.csv

hotspot_annotation:
hotspots:
checksum: 59fe5daf8039746c6690fce5e55d5115
path: design/Hotspots_combined_regions_nodups.csv
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/Hotspots_combined_regions_nodups.csv

hotspot_info:
hotspot_mutations:
checksum: 59fe5daf8039746c6690fce5e55d5115
path: design/Hotspots_combined_regions_nodups.csv
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/Hotspots_combined_regions_nodups.csv

hotspot_report:
hotspot_mutations:
checksum: 59fe5daf8039746c6690fce5e55d5115
path: design/Hotspots_combined_regions_nodups.csv
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/Hotspots_combined_regions_nodups.csv

manta_config_t:
extra:
checksum: b8f464f2af0d71c4e91fcdbd90378b6d
path: design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.210608.bed.gz
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.210608.bed.gz
extra_tbi:
checksum: 9c57e51d22b33d8683698d9c8d0c4b7a
path: design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.210608.bed.gz.tbi
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.210608.bed.gz.tbi

purecn:
intervals:
checksum: 0857e05962696cd3c2e5a4ea94d0fb2c
path: purecn/targets_twist-gms-st_hg19_25000_intervals.txt
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/targets_twist-gms-st_hg19_25000_intervals.txt

purecn_coverage:
intervals:
checksum: 0857e05962696cd3c2e5a4ea94d0fb2c
path: purecn/targets_twist-gms-st_hg19_25000_intervals.txt
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/cnv/targets_twist-gms-st_hg19_25000_intervals.txt

report_fusions:
annotation_bed:
checksum: af529c0ece5fe201de4d507000564ff7
path: rna_fusion/Twist_RNA_fusionpartners.bed
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/rna_fusion/Twist_RNA_fusionpartners.bed

references:
design_bed:
checksum: 06751f8685f1d507f4c48774450c0275
path: design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.reannotated.230222.bed
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.reannotated.230222.bed

design_intervals:
checksum: babb76d1e2490619eef47cf5b41db9f7
path: design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.210608.interval_list
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/pool1_pool2.sort.merged.padded20.cnv200.hg19.split_fusion_genes.MUC6_31_rm.exon_only.reannotated.210608.interval_list

design_intervals_gatk_cnv:
checksum: 812f9f89faf750d1948f19166056f1d1
path: design/pool1_pool2_nochr_3c.sort.merged.padded20.cnv400.hg19.210311.met.annotated.bed.preprocessed.interval_list
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/pool1_pool2_nochr_3c.sort.merged.padded20.cnv400.hg19.210311.met.annotated.bed.preprocessed.interval_list

design_intervals_rna:
checksum: c9cda4a99bccb8d3ac2d11503d8b83e1
path: design/Twist_RNA_Design5.annotated.interval_list
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/design/Twist_RNA_Design5.annotated.interval_list

report_gene_fuse:
filter_fusions:
checksum: b6bc58f14e2cee6e481f1cabf1fd2c0b
path: gene_fuse/filter_fusions_20230214.csv
type: file
url: https://github.com/genomic-medicine-sweden/Twist_Solid_pipeline_files/raw/v0.1.0/gene_fuse/filter_fusions_20230214.csv
9 changes: 9 additions & 0 deletions config/references/nextseq.hg19.pon.yaml
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db_string:
checksum: 076f3a9bec5e9941eb4bbbf4594c0037
path: SVDB/all_TN_292_svdb_0.8_20220505.vcf
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882898

purecn:
extra:
checksum: eb311461a92b53a9494bba9625ecd4c3
path: purecn/mapping_bias_nextseq_27_hg19.rds
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882865

normaldb:
checksum: d77528e5bfeec40791235e52dcbed7ef
path: purecn/normalDB_nextseq_27_hg19.rds
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882874


gatk_denoise_read_counts:
normal_reference:
checksum: eee609d42ca9ea071521664bdac6c4d6
path: PoN/gatk_cnv_nextseq_36.hdf5
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882859

cnvkit_batch:
normal_reference:
checksum: 2c8f519a872d92ec1cb43bd29518a71b
path: PoN/cnvkit_nextseq_36.cnn
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882850

cnvkit_batch_hrd:
normal_reference_hrd:
checksum: 89d2ca215b62651e5272a4bb70b7d217
path: PoN/cnvkit_nextseq_27_HRD.cnn
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882847

msisensor_pro:
PoN:
checksum: 23c9553c7043fff1a8428fcd3b231c60
path: PoN/Msisensor_pro_reference_nextseq_36.list_baseline
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882868

reference:
background:
checksum: 664471a52761adf69ed1f8310a60f445
path: Background/background_panel_nextseq_noUmea_27_dp500_af015.tsv
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882841

artifacts:
checksum: 73531299238e0a0884405a892e6789ac
path: Artifact/artifact_panel_nextseq_36.tsv
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882835
9 changes: 9 additions & 0 deletions config/references/novaseq.hg19.pon.yaml
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db_string:
checksum: 076f3a9bec5e9941eb4bbbf4594c0037
path: SVDB/all_TN_292_svdb_0.8_20220505.vcf
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882898

purecn:
extra:
checksum: eb311461a92b53a9494bba9625ecd4c3
path: purecn/mapping_bias_nextseq_27_hg19.rds
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882865

normaldb:
checksum: d77528e5bfeec40791235e52dcbed7ef
path: purecn/normalDB_nextseq_27_hg19.rds
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882874


gatk_denoise_read_counts:
normal_reference:
checksum: ab0a2f3276125c8695b72a2b2c5779ea
path: PoN/gatk_cnv_novaseq_13.hdf5
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882862

cnvkit_batch:
normal_reference:
checksum: e7853030e7a6b0ccbeffb7c008983a29
path: PoN/cnvkit_novaseq_13.cnn
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882853

cnvkit_batch_hrd:
normal_reference_hrd:
checksum: e7853030e7a6b0ccbeffb7c008983a29
path: PoN/cnvkit_novaseq_13_HRD.cnn
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882871

msisensor_pro:
PoN:
checksum: 40bda778c9208a366b39ec0e6cefde11
path: PoN/Msisensor_pro_reference_novaseq_13.list_baseline
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882871

reference:
background:
checksum: 563aa06990d90ed3ef33b4da1aac3c2e
path: Background/background_panel_novaseq_13_dp500_af015.tsv
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882844

artifacts:
checksum: 6d589735a4b922a6f7e852539f44a539
path: Artifact/artifact_panel_novaseq_13.tsv
type: file
url: https://figshare.scilifelab.se/ndownloader/files/40882838

8 changes: 7 additions & 1 deletion config/references/references.bianca.hg19.yaml
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fusioncatcher:
genome_path:
path: /sw/bioinfo/FusionCatcher/1.33/bianca/fusioncatcher/data/human_v102/
type: folder
path: /sw/bioinfo/FusionCatcher/1.33/bianca/fusioncatcher/data/human_v102/

reference:
fasta_rna:
path: /sw/data/CTAT_RESOURCE_LIB/2021-03/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa
type: file
# fai:
# path: /sw/data/CTAT_RESOURCE_LIB/2021-03/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai
# dict:
Expand All @@ -15,14 +17,18 @@
star:
extra:
path: /sw/data/reference/Homo_sapiens/GRCh37/program_files/lifescope/refGene/refGene.hg19.20101221.gtf
type: file
genome_index:
path: /sw/data/reference/Homo_sapiens/hg19/program_files/star/concat
type: file

star-fusion:
genome_path:
path: /sw/data/CTAT_RESOURCE_LIB/2021-03/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/
type: folder

vep:
vep_cache:
path: /sw/data/vep/107
type: folder

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