From b8fd25b0bf8212fbd1d0f78e2afad9b122dc4ebf Mon Sep 17 00:00:00 2001 From: Noronha Date: Fri, 19 Jan 2024 11:39:44 -0500 Subject: [PATCH 01/39] update metafusion to 1.0.2 --- modules/local/metafusion/container/Dockerfile | 4 ++-- modules/local/metafusion/main.nf | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/metafusion/container/Dockerfile b/modules/local/metafusion/container/Dockerfile index 018cef8..41c6e65 100755 --- a/modules/local/metafusion/container/Dockerfile +++ b/modules/local/metafusion/container/Dockerfile @@ -1,10 +1,10 @@ -FROM mapostolides/metafusion +FROM mapostolides/metafusion:latest LABEL author="Alexandria Dymun (pintoa1@mskcc.org)" \ maintainer="Anne Marie Noronha (noronhaa@mskcc.org)" \ version.image="0.0.6" -ENV METAFUSION_TAG="v1.0.1" +ENV METAFUSION_TAG="v1.0.2" ENV PATH="${PATH}:/MetaFusion/scripts" RUN R -e "chooseCRANmirror(ind=52); install.packages(c('plyr','data.table'))" diff --git a/modules/local/metafusion/main.nf b/modules/local/metafusion/main.nf index 40b90ee..c08ca38 100644 --- a/modules/local/metafusion/main.nf +++ b/modules/local/metafusion/main.nf @@ -3,8 +3,8 @@ process METAFUSION { label "process_low" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker://cmopipeline/metafusion:0.0.6' : - 'docker://cmopipeline/metafusion:0.0.6' }" + 'docker://cmopipeline/metafusion:0.0.7' : + 'docker://cmopipeline/metafusion:0.0.7' }" input: tuple val(meta), path(cff) From cc973421d0d79fd24221554b6730ff72bcbfce9e Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Fri, 19 Jan 2024 12:01:24 -0500 Subject: [PATCH 02/39] Clinical Transcripts Added to Params/metafusion, added clinical names to add flag function --- bin/Metafusion_forte.sh | 8 ++++++-- bin/add_flags_and_cluster_information.R | 4 +++- conf/igenomes.config | 1 + main.nf | 1 + modules/local/metafusion/main.nf | 2 ++ subworkflows/local/fusion.nf | 4 +++- 6 files changed, 16 insertions(+), 4 deletions(-) diff --git a/bin/Metafusion_forte.sh b/bin/Metafusion_forte.sh index 22f901e..9b3e59c 100755 --- a/bin/Metafusion_forte.sh +++ b/bin/Metafusion_forte.sh @@ -48,6 +48,10 @@ while test $# -gt 0;do recurrent_bedpe="$2" shift 2 ;; + --clinical_genes) + clinical_genes="$2" + shift 2 + ;; *) #OTHER_ARGUMENTS+=("$1") shift # Remove generic argument from processing @@ -79,10 +83,10 @@ cff=$outdir/$(basename $cff).renamed #Annotate cff if [ $genome_fasta ]; then echo Annotate cff, extract sequence surrounding breakpoint - reann_cff_fusion.py --cff $cff --gene_bed $gene_bed --ref_fa $genome_fasta > $outdir/$(basename $cff).reann.WITH_SEQ + reann_cff_fusion.py --cff $cff --gene_bed $gene_bed --ref_fa $genome_fasta --clinical_genes $clinical_genes > $outdir/$(basename $cff).reann.WITH_SEQ else echo Annotate cff, no extraction of sequence surrounding breakpoint - reann_cff_fusion.py --cff $cff --gene_bed $gene_bed > $outdir/$(basename $cff).reann.NO_SEQ + reann_cff_fusion.py --cff $cff --gene_bed $gene_bed --clinical_genes $clinical_genes > $outdir/$(basename $cff).reann.NO_SEQ fi # Assign .cff based on SEQ or NOSEQ diff --git a/bin/add_flags_and_cluster_information.R b/bin/add_flags_and_cluster_information.R index b74ff92..0482a79 100755 --- a/bin/add_flags_and_cluster_information.R +++ b/bin/add_flags_and_cluster_information.R @@ -57,7 +57,9 @@ library(data.table) "closest_exon3", "captured_reads", "gene5_transcript_id", - "gene3_transcript_id" + "gene3_transcript_id", + "is_clinical5", + "is_clinical3" ) colnames(unfiltered_cff) <- header_cff cluster <- fread(args[2],data.table = F) diff --git a/conf/igenomes.config b/conf/igenomes.config index 9cea106..c7bc481 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -33,6 +33,7 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" metafusion_gene_bed = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/v75_gene.bed.gz" metafusion_gene_info = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/gene_info_20230714.txt" + clinicalgenes = "/juno/work/ccs/pintoa1/jupyter_notebooks/clinical_bioinformatics_forte/clinical_transcripts_for_mane.txt" ensembl_version = 75 } 'GRCh38' { diff --git a/main.nf b/main.nf index c0a5e68..45f5bd5 100644 --- a/main.nf +++ b/main.nf @@ -28,6 +28,7 @@ params.metafusion_blocklist = WorkflowMain.getGenomeAttribute(params, 'metafus params.metafusion_gene_bed = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_bed') params.metafusion_gene_info = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_info') params.ensembl_version = WorkflowMain.getGenomeAttribute(params, 'ensembl_version') +params.clinicalgenes = WorkflowMain.getGenomeAttribute(params, 'clinicalgenes') /* diff --git a/modules/local/metafusion/main.nf b/modules/local/metafusion/main.nf index c08ca38..f725d0c 100644 --- a/modules/local/metafusion/main.nf +++ b/modules/local/metafusion/main.nf @@ -12,6 +12,7 @@ process METAFUSION { path info path fasta path blocklist + path clinicalgenes output: tuple val(meta), path("*final*cluster") , emit: cluster @@ -36,6 +37,7 @@ process METAFUSION { --gene_info $info \\ --genome_fasta $fasta \\ --recurrent_bedpe $blocklist \\ + --clinical_genes $clinicalgenes \\ ${args} cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf index 8c8bb3b..74ede69 100644 --- a/subworkflows/local/fusion.nf +++ b/subworkflows/local/fusion.nf @@ -35,6 +35,7 @@ workflow FUSION { fasta = params.fasta //gene_bed = params.metafusion_gene_bed gene_info = params.metafusion_gene_info + clinicalgenes = params.clinicalgenes //blocklist = params.metafusion_blocklist STAR_FOR_ARRIBA( @@ -113,7 +114,8 @@ workflow FUSION { gene_bed, gene_info, fasta, - blocklist + blocklist, + clinicalgenes ) ADD_FLAG( From 181ec3a1d3497e491adbd58532276b2b4e71e904 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Mon, 22 Jan 2024 11:39:03 -0500 Subject: [PATCH 03/39] add clinical whitelist to assests --- assets/clinical_whitelist.txt | 319 ++++++++++++++++++++++++++++++++++ conf/igenomes.config | 2 +- 2 files changed, 320 insertions(+), 1 deletion(-) create mode 100644 assets/clinical_whitelist.txt diff --git a/assets/clinical_whitelist.txt b/assets/clinical_whitelist.txt new file mode 100644 index 0000000..0b72c5a --- /dev/null +++ b/assets/clinical_whitelist.txt @@ -0,0 +1,319 @@ +gene_name ensembl_transcript refseq_transcript +AR ENST00000374690 NM_000044 +BTK ENST00000308731 NM_000061 +CDKN2A ENST00000304494 NM_000077 +EPOR ENST00000222139 NM_000121 +ESR1 ENST00000206249 NM_000125 +FGFR2 ENST00000358487 NM_000141 +FGFR3 ENST00000440486 NM_000142 +JAK3 ENST00000458235 NM_000215 +KIT ENST00000288135 NM_000222 +MET ENST00000397752 NM_000245 +PTCH1 ENST00000331920 NM_000264 +NME1 ENST00000393196 NM_000269 +RAG1 ENST00000299440 NM_000448 +GNAS ENST00000371085 NM_000516 +RAG2 ENST00000311485 NM_000536 +CD44 ENST00000428726 NM_000610 +CD79B ENST00000006750 NM_000626 +BCL2 ENST00000333681 NM_000633 +CSF1 ENST00000329608 NM_000757 +DCK ENST00000286648 NM_000788 +PGR ENST00000325455 NM_000926 +RARA ENST00000254066 NM_000964 +SS18 ENST00000415083 NM_001007559 +MYBL1 ENST00000522677 NM_001080416 +NUTM2A ENST00000381707 NM_001099338 +BCOR ENST00000378444 NM_001123385 +YAP1 ENST00000282441 NM_001130145 +MYB ENST00000341911 NM_001130173 +BIRC3 ENST00000263464 NM_001165 +MEAF6 ENST00000296214 NM_001270875 +NUTM2B ENST00000429828 NM_001278495 +EIF4A1 ENST00000293831 NM_001416 +ID4 ENST00000378700 NM_001546 +ACVR2A ENST00000241416 NM_001616 +ARAF ENST00000377045 NM_001654 +RHOA ENST00000418115 NM_001664 +BCL6 ENST00000406870 NM_001706 +BMP7 ENST00000395863 NM_001719 +CCND2 ENST00000261254 NM_001759 +CCND3 ENST00000372991 NM_001760 +ENTPD1 ENST00000371205 NM_001776 +CDC25A ENST00000302506 NM_001789 +CEBPE ENST00000206513 NM_001805 +CEBPG ENST00000284000 NM_001806 +ERBB3 ENST00000267101 NM_001982 +ETV6 ENST00000396373 NM_001987 +FOXO1 ENST00000379561 NM_002015 +FLT1 ENST00000282397 NM_002019 +GATA1 ENST00000376670 NM_002049 +IRF8 ENST00000268638 NM_002163 +IDH2 ENST00000330062 NM_002168 +IL7R ENST00000303115 NM_002185 +ITPKB ENST00000429204 NM_002221 +JAK1 ENST00000342505 NM_002227 +LMO1 ENST00000335790 NM_002315 +LTK ENST00000263800 NM_002344 +MAL ENST00000309988 NM_002371 +MN1 ENST00000302326 NM_002430 +IRF4 ENST00000380956 NM_002460 +MYH11 ENST00000300036 NM_002474 +NPM1 ENST00000296930 NM_002520 +NRAS ENST00000369535 NM_002524 +NTRK1 ENST00000524377 NM_002529 +PBX1 ENST00000420696 NM_002585 +PDGFB ENST00000331163 NM_002608 +PDGFRB ENST00000261799 NM_002609 +PIM1 ENST00000373509 NM_002648 +PLAG1 ENST00000316981 NM_002655 +PPAT ENST00000264220 NM_002703 +PRKACA ENST00000308677 NM_002730 +PRKAR2B ENST00000265717 NM_002736 +PRKCA ENST00000413366 NM_002737 +PRKD1 ENST00000331968 NM_002742 +MAP2K1 ENST00000307102 NM_002755 +PTPN1 ENST00000371621 NM_002827 +PTPN11 ENST00000351677 NM_002834 +RAF1 ENST00000251849 NM_002880 +SOX11 ENST00000322002 NM_003108 +SRF ENST00000265354 NM_003131 +STAT6 ENST00000300134 NM_003153 +TCF3 ENST00000262965 NM_003200 +TNFSF4 ENST00000281834 NM_003326 +TYK2 ENST00000525621 NM_003331 +XPO1 ENST00000401558 NM_003400 +HMGA2 ENST00000403681 NM_003483 +TP63 ENST00000264731 NM_003722 +RAB7L1 ENST00000367139 NM_003929 +NFKB1 ENST00000226574 NM_003998 +BCL2A1 ENST00000267953 NM_004049 +DNTT ENST00000371174 NM_004088 +E2F2 ENST00000361729 NM_004091 +FLT3 ENST00000241453 NM_004119 +ALK ENST00000389048 NM_004304 +BCR ENST00000305877 NM_004327 +CALR ENST00000316448 NM_004343 +CEBPA ENST00000498907 NM_004364 +CREBBP ENST00000262367 NM_004380 +ERBB2 ENST00000269571 NM_004448 +ETV5 ENST00000306376 NM_004454 +EZH2 ENST00000320356 NM_004456 +SH3BP5 ENST00000383791 NM_004844 +NRG2 ENST00000361474 NM_004883 +CDKN2B ENST00000276925 NM_004936 +ETV1 ENST00000430479 NM_004956 +FUS ENST00000254108 NM_004960 +JAK2 ENST00000381652 NM_004972 +KRAS ENST00000311936 NM_004985 +PDCD1 ENST00000334409 NM_005018 +NUP214 ENST00000359428 NM_005085 +ABL1 ENST00000318560 NM_005157 +BCL3 ENST00000164227 NM_005178 +CBL ENST00000264033 NM_005188 +CEBPD ENST00000408965 NM_005195 +EGFR ENST00000275493 NM_005228 +ERBB4 ENST00000342788 NM_005235 +EWSR1 ENST00000397938 NM_005243 +FGR ENST00000374005 NM_005248 +FOS ENST00000303562 NM_005252 +GLI1 ENST00000228682 NM_005269 +GRB7 ENST00000309156 NM_005310 +MPL ENST00000372470 NM_005373 +SH2B3 ENST00000341259 NM_005475 +TLX1 ENST00000370196 NM_005521 +LMO2 ENST00000257818 NM_005574 +LYL1 ENST00000264824 NM_005583 +MUSK ENST00000374448 NM_005592 +TMPRSS2 ENST00000332149 NM_005656 +PRKD3 ENST00000234179 NM_005813 +IDH1 ENST00000345146 NM_005896 +IKZF1 ENST00000331340 NM_006060 +TFG ENST00000240851 NM_006070 +DNAJB1 ENST00000254322 NM_006145 +NFE2L2 ENST00000397062 NM_006164 +NTRK2 ENST00000277120 NM_006180 +PDGFRA ENST00000257290 NM_006206 +PIK3CA ENST00000263967 NM_006218 +TFE3 ENST00000315869 NM_006521 +NCOA2 ENST00000452400 NM_006540 +FOSB ENST00000353609 NM_006732 +U2AF1 ENST00000291552 NM_006758 +YWHAE ENST00000264335 NM_006761 +KAT6A ENST00000265713 NM_006766 +PIM2 ENST00000376509 NM_006875 +DNMT3B ENST00000328111 NM_006892 +PYCR1 ENST00000329875 NM_006907 +PICALM ENST00000393346 NM_007166 +BRD3 ENST00000303407 NM_007371 +CHIC2 ENST00000263921 NM_012110 +MGEA5 ENST00000361464 NM_012215 +NFATC2 ENST00000371564 NM_012340 +RLF ENST00000372771 NM_012421 +SF3B1 ENST00000335508 NM_012433 +STAT5B ENST00000293328 NM_012448 +TNFRSF13B ENST00000261652 NM_012452 +IKZF3 ENST00000346872 NM_012481 +FAM216A ENST00000377673 NM_013300 +BLNK ENST00000224337 NM_013314 +CD274 ENST00000381577 NM_014143 +SETD2 ENST00000409792 NM_014159 +LIMD1 ENST00000273317 NM_014240 +NEK6 ENST00000320246 NM_014397 +KIAA0101 ENST00000300035 NM_014736 +MAST1 ENST00000251472 NM_014975 +CAMTA1 ENST00000303635 NM_015215 +WWTR1 ENST00000360632 NM_015472 +VGLL3 ENST00000398399 NM_016206 +CYB5R2 ENST00000299498 NM_016229 +KLF2 ENST00000248071 NM_016270 +NUP98 ENST00000324932 NM_016320 +PAX5 ENST00000358127 NM_016734 +MBTD1 ENST00000586178 NM_017643 +EXOC2 ENST00000230449 NM_018303 +STRBP ENST00000348403 NM_018387 +PAG1 ENST00000220597 NM_018440 +BATF3 ENST00000243440 NM_018664 +MAML3 ENST00000509479 NM_018717 +AICDA ENST00000229335 NM_020661 +RET ENST00000355710 NM_020975 +LZTS1 ENST00000381569 NM_021020 +TLX3 ENST00000296921 NM_021025 +RELA ENST00000406246 NM_021975 +THADA ENST00000405975 NM_022065 +PRDM16 ENST00000270722 NM_022114 +RBM15 ENST00000369784 NM_022768 +CBFB ENST00000412916 NM_022845 +WHSC1L1 ENST00000317025 NM_023034 +FGFR1 ENST00000447712 NM_023110 +EBF1 ENST00000313708 NM_024007 +PHF1 ENST00000374516 NM_024165 +NOTCH2 ENST00000256646 NM_024408 +PDGFD ENST00000393158 NM_025208 +PDCD1LG2 ENST00000397747 NM_025239 +ZCCHC7 ENST00000336755 NM_032226 +CARD11 ENST00000396946 NM_032415 +MAML2 ENST00000524717 NM_032427 +GLIS2 ENST00000433375 NM_032575 +GATA2 ENST00000341105 NM_032638 +RSPO3 ENST00000356698 NM_032784 +CCNB3 ENST00000376042 NM_033031 +CCND1 ENST00000227507 NM_053056 +BCL11B ENST00000357195 NM_138576 +BAX ENST00000345358 NM_138761 +TAF15 ENST00000605844 NM_139215 +HOXA9 ENST00000343483 NM_152739 +PTK2B ENST00000346049 NM_173176 +JAZF1 ENST00000283928 NM_175061 +P2RY8 ENST00000381297 NM_178129 +RSPO2 ENST00000276659 NM_178565 +VGLL2 ENST00000326274 NM_182645 +PRKACB ENST00000370685 NM_182948 +CREB3L2 ENST00000330387 NM_194071 +TERT ENST00000310581 NM_198253 +SS18L1 ENST00000331758 NM_198935 +AKT1 ENST00000555528 NM_005163 +AR ENST00000396043 NM_001011645 +ARHGAP26 ENST00000274498 NM_015071 +BCORL1 ENST00000540052 NM_021946 +BRAF ENST00000288602 NM_004333 +BRD4 ENST00000263377 NM_058243 +CIC ENST00000575354 NM_015125 +CSF1 ENST00000369802 NM_172212 +DEK ENST00000397239 NM_003472 +EPC1 ENST00000263062 NM_025209 +ERG ENST00000417133 NM_004449 +ESR1 ENST00000440973 NM_001122742 +ETV4 ENST00000319349 NM_001986 +FGF1 ENST00000378046 NM_00800 +FGFR1 ENST00000397091 NM_015850 +FGFR4 ENST00000292408 NM_002011 +GRM1 ENST00000492807 NM_001278065 +IGF1R ENST00000268035 NM_000875 +LTK ENST00000453182 NM_001135685 +MKL2 ENST00000574045 NM_014048 +NCOA1 ENST00000288599 NM_147223 +NCOA3 ENST00000372004 NM_006534 +NOTCH1 ENST00000277541 NM_017617 +NR4A3 ENST00000330847 NM_173200 +NRG1 ENST00000522402 NM_001159996 +NRG1 ENST00000341377 NM_004495 +NRG1 ENST00000356819 NM_013956 +NRG1 ENST00000287842 NM_013957 +NRG1 ENST00000520502 NM_013959 +NRG1 ENST00000520407 NM_013962 +NTRK1 ENST00000392302 NM_001007792 +NTRK3 ENST00000317501 NM_001007156 +NTRK3 ENST00000317501 NM_002530 +NUTM1 ENST00000333756 NM_175741 +PAX3 ENST00000392069 NM_181459 +PAX7 ENST00000375375 NM_002584 +PPARG ENST00000287820 NM_015869 +PRB3 ENST00000381842 NM_006249 +PRKCB ENST00000303531 NM_002738 +PRKD2 ENST00000433867 NM_016457 +RAD51B ENST00000487270 NM_133509 +RET ENST00000340058 NM_020630 +ROS1 ENST00000368508 NM_002944 +SS18 ENST00000269137 NM_005637 +STAT6 ENST00000300134 NM_001178078 +TCF12 ENST00000438423 NM_207036 +TFEB ENST00000230323 NM_007162 +TMPRSS2 ENST00000398585 NM_001135099 +USP6 ENST00000574788 NM_004505 +AKT3 ENST00000366539 NM_005465 +ASXL1 ENST00000375687 NM_015338 +CCDC50 ENST00000392455 NM_174908 +CHD1 ENST00000284049 NM_001270 +CIITA ENST00000324288 NM_000246 +CRLF2 ENST00000400841 NM_022148 +CSF1R ENST00000286301 NM_005211 +CTLA4 ENST00000302823 NM_005214 +DLEU1 ENST00000378180 NR_002605 +FOXP1 ENST00000318789 NM_032682 +FUT8 ENST00000557164 NM_004480 +IL16 ENST00000394652 NM_004513 +KDM6A ENST00000377967 NM_021140 +LRMP ENST00000354454 NM_006152 +MALT1 ENST00000348428 NM_006785 +MECOM ENST00000494292 NM_004991 +MKL1 ENST00000355630 NM_020831 +MLF1 ENST00000355893 NM_022443 +MLLT4 ENST00000392108 NM_001040000 +MUC1 ENST00000337604 NM_002456 +MYC ENST00000377970 NM_002467 +MYD88 ENST00000396334 NM_002468 +NFKB2 ENST00000189444 NM_002502 +PLCG1 ENST00000244007 NM_002660 +PLCG2 ENST00000359376 NM_002661 +RANBP1 ENST00000331821 NM_002882 +RUNX1 ENST00000300305 NM_001754 +S1PR2 ENST00000590320 NM_004230 +SEMA6A ENST00000343348 NM_020796 +SERPINA9 ENST00000337425 NM_175739 +SETBP1 ENST00000282030 NM_015559 +TAL1 ENST00000371884 NM_003189 +WT1 ENST00000332351 NM_000378 +ABL2 ENST00000512653 NM_005158 +ASB13 ENST00000479033 NR_0024581 +BMF ENST00000354670 NM_033503 +CDK6 ENST00000265734 NM_001259 +CSF3R ENST00000373103 NM_156039 +DENND3 ENST00000519811 NM_014957 +DNM2 ENST00000389253 NM_004945 +DNMT3A ENST00000321117 NM_175629 +DUSP22 ENST00000344450 NM_020185 +FBXW7 ENST00000281708 NM_033632 +IKZF2 ENST00000457361 NM_016260 +KMT2A ENST00000534358 NM_005933 +MLLT10 ENST00000377072 NM_004641 +MME ENST00000460393 NM_000902 +NF1 ENST00000358273 NM_000267 +NT5C2 ENST00000343289 NM_012229 +PAICS ENST00000264221 NM_006452 +PHF6 ENST00000370800 NM_032335 +PML ENST00000395135 NM_002675 +SLC29A1 ENST00000427851 NM_001078175 +SRSF2 ENST00000359995 NM_003016 +STAT3 ENST00000404395 NM_003150 +STIL ENST00000360380 NM_003035 diff --git a/conf/igenomes.config b/conf/igenomes.config index c7bc481..3884405 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -33,7 +33,7 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" metafusion_gene_bed = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/v75_gene.bed.gz" metafusion_gene_info = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/gene_info_20230714.txt" - clinicalgenes = "/juno/work/ccs/pintoa1/jupyter_notebooks/clinical_bioinformatics_forte/clinical_transcripts_for_mane.txt" + clinicalgenes = "assets/clinical_whitelist.txt" ensembl_version = 75 } 'GRCh38' { From 0b3e0199c6af54fa710b6c646fb82781fc6b2f52 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Fri, 26 Jan 2024 15:40:32 -0500 Subject: [PATCH 04/39] Update igenomes.config assets --- conf/igenomes.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 3884405..460e6e4 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -33,7 +33,7 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" metafusion_gene_bed = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/v75_gene.bed.gz" metafusion_gene_info = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/gene_info_20230714.txt" - clinicalgenes = "assets/clinical_whitelist.txt" + clinicalgenes = "$projectDir/assets/clinical_whitelist.txt" ensembl_version = 75 } 'GRCh38' { From ddc4f493a88c5a36b293c7b37123490b04b944d4 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Fri, 26 Jan 2024 15:41:03 -0500 Subject: [PATCH 05/39] Update igenomes.config --- conf/igenomes.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 460e6e4..cf6026a 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -33,7 +33,7 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" metafusion_gene_bed = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/v75_gene.bed.gz" metafusion_gene_info = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/gene_info_20230714.txt" - clinicalgenes = "$projectDir/assets/clinical_whitelist.txt" + clinicalgenes = "${workflow.projectDir}/assets/clinical_whitelist.txt" ensembl_version = 75 } 'GRCh38' { From 0c40229756eed304241b300b46be507cd6896647 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Mon, 29 Jan 2024 10:29:58 -0500 Subject: [PATCH 06/39] Update igenomes.config --- conf/igenomes.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index cf6026a..0882bf7 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -33,7 +33,7 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" metafusion_gene_bed = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/v75_gene.bed.gz" metafusion_gene_info = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/gene_info_20230714.txt" - clinicalgenes = "${workflow.projectDir}/assets/clinical_whitelist.txt" + clinicalgenes = "${projectDir}/assets/clinical_whitelist.txt" ensembl_version = 75 } 'GRCh38' { From c52013b4f25bd8172477a5211a338f156bc39d49 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Fri, 19 Apr 2024 12:45:02 -0400 Subject: [PATCH 07/39] terra configuration for references --- conf/terra.config | 63 +++++++++++++++++++++++++++++++++++++++++++++++ nextflow.config | 1 + 2 files changed, 64 insertions(+) create mode 100644 conf/terra.config diff --git a/conf/terra.config b/conf/terra.config new file mode 100644 index 0000000..737b328 --- /dev/null +++ b/conf/terra.config @@ -0,0 +1,63 @@ +executor { + name = "lsf" + queueSize = 5000000000 + perJobMemLimit = true +} + +process { + memory = "8.GB" + time = { 3.h * task.attempt } + clusterOptions = "" + scratch = true + beforeScript = "module load singularity/3.1.1; unset R_LIBS; catch_term () { echo 'caught USR2/TERM signal'; set +e; false; on_exit ; } ; trap catch_term USR2 TERM" + errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } + maxRetries = 3 + + withLabel:process_single { + cpus = { check_max( 1, 'cpus' ) } + memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } + time = { check_max( 4.h * task.attempt, 'time' ) } + } + withLabel:process_low { + cpus = { check_max( 2 * task.attempt, 'cpus' ) } + memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } + time = { check_max( 4.h * task.attempt, 'time' ) } + } + withLabel:process_medium { + cpus = { check_max( 6 * task.attempt, 'cpus' ) } + memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } + time = { check_max( 8.h * task.attempt, 'time' ) } + } + withLabel:process_high { + cpus = { check_max( 12 * task.attempt, 'cpus' ) } + memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } + time = { check_max( 16.h * task.attempt, 'time' ) } + } + withLabel:process_high_memory { + memory = { round_memory( check_max( 200.GB * task.cpus, 'memory' )/task.cpus, "down") } + } + withLabel:process_low { + time = { check_max( 50.h * task.attempt, 'time' ) } + } +} + +params { + max_memory = "128.GB" + max_cpus = 24 + max_time = "500.h" + mem_per_core = true + reference_base = "/juno/work/ccs/cmopipeline/forte" + igenomes_base = '/juno/cmo/tempo/cmopipeline/mskcc-igenomes/igenomes' + targets_base = '/juno/work/ccs/cmopipeline/forte' +} + +env { + SPARK_LOCAL_DIRS = './' +} + +singularity { + enabled = true + runOptions = "-B $TMPDIR" + autoMounts = true + cacheDir = "/juno/cmo/tempo/cmopipeline/singularity_images/" +} diff --git a/nextflow.config b/nextflow.config index be9b870..f8d0a9b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -141,6 +141,7 @@ profiles { } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } + terra { includeConfig 'conf/terra.config' } juno { includeConfig 'conf/juno.config' } } From e987538a359a3032d45607d18688e5336be0f125 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Tue, 30 Apr 2024 15:09:45 -0400 Subject: [PATCH 08/39] mrge prepare metafusion references and update metafusion --- bin/final_generate_v75_gene_bed.R | 20 ++++++++++++++++++-- conf/igenomes.config | 1 + subworkflows/local/prepare_references.nf | 6 +++++- 3 files changed, 24 insertions(+), 3 deletions(-) diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index ffcb064..0749c84 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -16,12 +16,21 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") +<<<<<<< Updated upstream message("final_generate_v75_gene_bed.R ") } args = commandArgs(TRUE) if (length(args)!=2) { +======= + message("final_generate_v75_gene_bed.R ") +} + +args = commandArgs(TRUE) + +if (length(args)!=3) { +>>>>>>> Stashed changes usage() quit() } @@ -35,8 +44,15 @@ if (length(args)!=2) { gtf <- rtracklayer::import(args[1]) gtf_df <- as.data.frame(gtf) - -file.to_write <- args[2] +#remove incomplete transcripts mRNA_end_NF and mRNA_start_NF (not finished) +gtf_df <- gtf_df[!grepl("NF",gtf_df$tag),] +#Add transcript version corresponding to gtf ensembl version +transcripts <- read.delim(args[2],header = F) +transcripts <- transcripts[,c("V15","V16")] +gtf_df <- merge(gtf_df, transcripts, by.x = "transcript_id",by.y = "V15") +gtf_df$transcript_id <- paste0(gtf_df$transcript_id,".",gtf_df$V16) + +file.to_write <- args[3] gtf_df <- gtf_df %>% rename( diff --git a/conf/igenomes.config b/conf/igenomes.config index 3632fc1..6729a49 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -33,6 +33,7 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" clinicalgenes = "${projectDir}/assets/clinical_whitelist.txt" ensembl_version = 75 + transcripts = "https://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_core_75_37/transcript.txt.gz" } 'GRCh38' { fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index b51a3cd..13db571 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -84,13 +84,17 @@ workflow PREPARE_REFERENCES { ARRIBA_DOWNLOAD() + //cosmic_usr = params.cosmic_usr ?: "" + //cosmic_passwd = params.cosmic_passwd ?: "" + AGAT_SPADDINTRONS( [[:],gtf], [] ) METAFUSION_GENEBED( - AGAT_SPADDINTRONS.out.gff + AGAT_SPADDINTRONS.out.gff, + params.transcripts ) METAFUSION_GENEINFO( From efe528e96fb0f040f6e0f45bde5ee2281995b068 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Thu, 2 May 2024 12:41:10 -0400 Subject: [PATCH 09/39] modify metafusion transcripts to include transcript version --- bin/final_generate_v75_gene_bed.R | 9 --------- conf/terra.config | 2 +- main.nf | 4 ++-- modules/local/metafusion/genebed/main.nf | 2 ++ .../usr/bin/final_generate_v75_gene_bed.R | 19 +++++++++++++------ 5 files changed, 18 insertions(+), 18 deletions(-) diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index 0749c84..2d8c381 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -16,21 +16,12 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") -<<<<<<< Updated upstream - message("final_generate_v75_gene_bed.R ") -} - -args = commandArgs(TRUE) - -if (length(args)!=2) { -======= message("final_generate_v75_gene_bed.R ") } args = commandArgs(TRUE) if (length(args)!=3) { ->>>>>>> Stashed changes usage() quit() } diff --git a/conf/terra.config b/conf/terra.config index 737b328..643cd7b 100644 --- a/conf/terra.config +++ b/conf/terra.config @@ -15,7 +15,7 @@ process { withLabel:process_single { cpus = { check_max( 1, 'cpus' ) } - memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } + memory = { round_memory( check_max( 8.GB * task.cpus * task.attempt, 'memory' )/task.cpus, "down") } time = { check_max( 4.h * task.attempt, 'time' ) } } withLabel:process_low { diff --git a/main.nf b/main.nf index 45f5bd5..de37dd9 100644 --- a/main.nf +++ b/main.nf @@ -28,8 +28,8 @@ params.metafusion_blocklist = WorkflowMain.getGenomeAttribute(params, 'metafus params.metafusion_gene_bed = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_bed') params.metafusion_gene_info = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_info') params.ensembl_version = WorkflowMain.getGenomeAttribute(params, 'ensembl_version') -params.clinicalgenes = WorkflowMain.getGenomeAttribute(params, 'clinicalgenes') - +params.clinicalgenes = WorkflowMain.getGenomeAttribute(params, 'clinicalgenes') +params.transcripts = WorkflowMain.getGenomeAttribute(params, 'transcripts') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 2314c40..72b1a2f 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -9,6 +9,7 @@ process METAFUSION_GENEBED { input: tuple val(meta), path(gff) + path(transcripts) output: tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed @@ -23,6 +24,7 @@ process METAFUSION_GENEBED { """ final_generate_v75_gene_bed.R \\ $gff \\ + $transcripts \\ ${prefix}.metafusion.gene.bed cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R index 46a5d15..2d8c381 100755 --- a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R +++ b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R @@ -1,5 +1,5 @@ - #!/usr/local/bin/Rscript + # __author__ = "Alexandria Dymun" # __email__ = "pintoa1@mskcc.org" # __contributor__ = "Anne Marie Noronha (noronhaa@mskcc.org)" @@ -8,7 +8,7 @@ suppressPackageStartupMessages({ - library(plyr) +# library(plyr) library(dplyr) library(data.table) library(stringr) @@ -16,12 +16,12 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") - message("final_generate_v75_gene_bed.R ") + message("final_generate_v75_gene_bed.R ") } args = commandArgs(TRUE) -if (length(args)!=2) { +if (length(args)!=3) { usage() quit() } @@ -35,8 +35,15 @@ if (length(args)!=2) { gtf <- rtracklayer::import(args[1]) gtf_df <- as.data.frame(gtf) - -file.to_write <- args[2] +#remove incomplete transcripts mRNA_end_NF and mRNA_start_NF (not finished) +gtf_df <- gtf_df[!grepl("NF",gtf_df$tag),] +#Add transcript version corresponding to gtf ensembl version +transcripts <- read.delim(args[2],header = F) +transcripts <- transcripts[,c("V15","V16")] +gtf_df <- merge(gtf_df, transcripts, by.x = "transcript_id",by.y = "V15") +gtf_df$transcript_id <- paste0(gtf_df$transcript_id,".",gtf_df$V16) + +file.to_write <- args[3] gtf_df <- gtf_df %>% rename( From d227e1ea9e7f83bd749748c782831afe2c6d6cb9 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Thu, 2 May 2024 16:07:32 -0400 Subject: [PATCH 10/39] move adding transcript versions to during cff annotate so agfusion can run --- bin/add_annotations_cff.R | 34 +++++++++++++++++++++--- bin/final_generate_v75_gene_bed.R | 11 +++----- modules/local/cff_annotate/main.nf | 6 +++-- modules/local/metafusion/genebed/main.nf | 2 -- subworkflows/local/fusion.nf | 7 +++-- subworkflows/local/prepare_references.nf | 3 +-- 6 files changed, 43 insertions(+), 20 deletions(-) diff --git a/bin/add_annotations_cff.R b/bin/add_annotations_cff.R index 25c030d..d77ed77 100755 --- a/bin/add_annotations_cff.R +++ b/bin/add_annotations_cff.R @@ -1,7 +1,7 @@ #!/usr/local/bin/Rscript # __author__ = "Anne Marie Noronha" # __email__ = "noronhaa@mskcc.org" -# __version__ = "0.0.1" +# __version__ = "0.0.2" suppressPackageStartupMessages({ @@ -11,7 +11,7 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") - message("add_annotations_cff.R --cff-file --agfusion-file --oncokb-file --out-prefix ") + message("add_annotations_cff.R --cff-file --agfusion-file --oncokb-file --out-prefix --transcripts ") } args = commandArgs(TRUE) @@ -39,14 +39,14 @@ parse_args <- function(x){ args_opt <- parse_args(paste(args,collapse=" ")) -possible_args = c("cff", "oncokb", "agfusion", "out_prefix") +possible_args = c("cff", "oncokb", "agfusion", "out_prefix","transcripts") if (length(setdiff(names(args_opt),possible_args)) > 0){ message("Invalid options") usage() quit() } -required_args <- c("cff","agfusion","out_prefix") +required_args <- c("cff","agfusion","out_prefix","transcripts") if (length(setdiff(required_args,names(args_opt))) > 0) { message("Missing required arguments") usage() @@ -57,11 +57,17 @@ oncokb_file = args_opt$oncokb agfusion_file = args_opt$agfusion cff_file = args_opt$cff out_prefix = args_opt$out_prefix +transcripts = args_opt$transcripts cff = fread(cff_file) final_cff_cols <- c(names(cff)) agfusion_tab = fread(agfusion_file) %>% select(c(`5'_transcript`,`3'_transcript`,`5'_breakpoint`,`3'_breakpoint`,Fusion_effect)) +#Add transcript version corresponding to gtf ensembl version +transcripts <- read.delim(transcripts,header = F) +transcripts <- transcripts[,c("V15","V16")] + final_cff_cols <- c(final_cff_cols,"Fusion_effect") + if (!is.null(oncokb_file)){ oncokb_tab = fread(oncokb_file) %>% select(-Fusion) final_cff_cols = c(final_cff_cols,names(oncokb_tab %>% select(-Tumor_Sample_Barcode))) @@ -74,6 +80,26 @@ if (!is.null(oncokb_file)){ all.y=F ) } +### merge +cff <- merge( + cff, + transcripts, + by.x = "gene3_transcript_id", + by.y = "V15", + all.x = T , + all.y = F) +cff$gene3_transcript_id <- paste0(cff$gene3_transcript_id,".",cff$V16) +cff$V16 <- NULL +cff <- merge( + cff, + transcripts, + by.x = "gene5_transcript_id", + by.y = "V15", + all.x = T, + all.y = F) + +cff$gene5_transcript_id <- paste0(cff$gene5_transcript_id,".",cff$V16) +cff$V16 <- NULL cff <- merge( cff, diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index 2d8c381..17caadc 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -16,12 +16,12 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") - message("final_generate_v75_gene_bed.R ") + message("final_generate_v75_gene_bed.R ") } args = commandArgs(TRUE) -if (length(args)!=3) { +if (length(args)!=2) { usage() quit() } @@ -37,13 +37,8 @@ gtf <- rtracklayer::import(args[1]) gtf_df <- as.data.frame(gtf) #remove incomplete transcripts mRNA_end_NF and mRNA_start_NF (not finished) gtf_df <- gtf_df[!grepl("NF",gtf_df$tag),] -#Add transcript version corresponding to gtf ensembl version -transcripts <- read.delim(args[2],header = F) -transcripts <- transcripts[,c("V15","V16")] -gtf_df <- merge(gtf_df, transcripts, by.x = "transcript_id",by.y = "V15") -gtf_df$transcript_id <- paste0(gtf_df$transcript_id,".",gtf_df$V16) -file.to_write <- args[3] +file.to_write <- args[2] gtf_df <- gtf_df %>% rename( diff --git a/modules/local/cff_annotate/main.nf b/modules/local/cff_annotate/main.nf index d96216c..c2d2e31 100644 --- a/modules/local/cff_annotate/main.nf +++ b/modules/local/cff_annotate/main.nf @@ -8,6 +8,7 @@ process CFF_ANNOTATE { input: tuple val(meta), path(cff), path(oncokb), path(agfusion) + path(transcripts) output: tuple val(meta), path("${prefix}.unfiltered.cff"), emit: unfiltered_cff @@ -25,12 +26,13 @@ process CFF_ANNOTATE { --cff ${cff} \\ ${oncokb_param} \\ --agfusion ${agfusion} \\ - --out-prefix ${prefix} + --out-prefix ${prefix} \\ + --transcripts ${transcripts} cat <<-END_VERSIONS > versions.yml "${task.process}": R: \$(R --version | head -n1) - add_annotations_cff.R: 0.0.1 + add_annotations_cff.R: 0.0.2 END_VERSIONS """ } diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 72b1a2f..2314c40 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -9,7 +9,6 @@ process METAFUSION_GENEBED { input: tuple val(meta), path(gff) - path(transcripts) output: tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed @@ -24,7 +23,6 @@ process METAFUSION_GENEBED { """ final_generate_v75_gene_bed.R \\ $gff \\ - $transcripts \\ ${prefix}.metafusion.gene.bed cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf index 2e86ae1..ec3e808 100644 --- a/subworkflows/local/fusion.nf +++ b/subworkflows/local/fusion.nf @@ -37,6 +37,7 @@ workflow FUSION { //gene_bed = params.metafusion_gene_bed clinicalgenes = params.clinicalgenes //blocklist = params.metafusion_blocklist + transcripts = params.transcripts STAR_FOR_ARRIBA( reads, @@ -140,7 +141,8 @@ workflow FUSION { CFF_FINALIZE( ADD_FLAG.out.unfiltered_cff .join(ONCOKB_FUSIONANNOTATOR.out.oncokb_fusions, by:0) - .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0) + .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0), + transcipts ) } else { CFF_FINALIZE( @@ -148,7 +150,8 @@ workflow FUSION { .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0) .map{ meta, cff, agfusion_file -> [ meta, cff, [], agfusion_file ] - } + }, + transcripts ) } ch_versions = ch_versions.mix(ADD_FLAG.out.versions.first()) diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index 13db571..0040943 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -93,8 +93,7 @@ workflow PREPARE_REFERENCES { ) METAFUSION_GENEBED( - AGAT_SPADDINTRONS.out.gff, - params.transcripts + AGAT_SPADDINTRONS.out.gff ) METAFUSION_GENEINFO( From 791241f533505a9e58b5d629b044928a3329cae9 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Thu, 2 May 2024 16:50:18 -0400 Subject: [PATCH 11/39] editor config --- bin/add_annotations_cff.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/add_annotations_cff.R b/bin/add_annotations_cff.R index d77ed77..7fbd530 100755 --- a/bin/add_annotations_cff.R +++ b/bin/add_annotations_cff.R @@ -80,7 +80,7 @@ if (!is.null(oncokb_file)){ all.y=F ) } -### merge +### merge cff <- merge( cff, transcripts, From a4a71a4891c170abe83735f3d35c9c494a1fdba5 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Fri, 3 May 2024 10:32:39 -0400 Subject: [PATCH 12/39] move merge of transcripts to after merge with agfusion --- bin/add_annotations_cff.R | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/bin/add_annotations_cff.R b/bin/add_annotations_cff.R index 7fbd530..97ceb57 100755 --- a/bin/add_annotations_cff.R +++ b/bin/add_annotations_cff.R @@ -80,6 +80,15 @@ if (!is.null(oncokb_file)){ all.y=F ) } + +cff <- merge( + cff, + agfusion_tab, + by.x = c("gene5_transcript_id","gene3_transcript_id","gene5_breakpoint","gene3_breakpoint"), + by.y = c("5'_transcript","3'_transcript","5'_breakpoint","3'_breakpoint"), + all.x = T, + all.y = T +) ### merge cff <- merge( cff, @@ -101,15 +110,6 @@ cff <- merge( cff$gene5_transcript_id <- paste0(cff$gene5_transcript_id,".",cff$V16) cff$V16 <- NULL -cff <- merge( - cff, - agfusion_tab, - by.x = c("gene5_transcript_id","gene3_transcript_id","gene5_breakpoint","gene3_breakpoint"), - by.y = c("5'_transcript","3'_transcript","5'_breakpoint","3'_breakpoint"), - all.x = T, - all.y = T -) - cff <- as.data.frame(cff)[,c(final_cff_cols)] #cff <- cff %>% mutate(!!final_cff_cols[34] := Fusion_effect) %>% select(-c(Fusion_effect)) From 5ac50c3bfa8338c0b5086556804e9af9595e7755 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc Date: Fri, 3 May 2024 11:09:40 -0400 Subject: [PATCH 13/39] try to resolve pr conflicts --- conf/igenomes.config | 3 ++- docs/output.md | 2 +- docs/usage.md | 1 - 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 6729a49..81770ab 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -50,7 +50,8 @@ params { cdna = "http://ftp.ensemblgenomes.org/pub/viruses/fasta/sars_cov_2/cdna/Sars_cov_2.ASM985889v3.cdna.all.fa.gz" metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37_test/blocklist_breakpoints.bedpe" ensembl_version = 75 - + clinicalgenes = "${projectDir}/assets/clinical_whitelist.txt" + transcripts = "https://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_core_75_37/transcript.txt.gz" } /* 'hg38' { diff --git a/docs/output.md b/docs/output.md index b5875d8..8e953c3 100644 --- a/docs/output.md +++ b/docs/output.md @@ -81,7 +81,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d -[featureCounts]([https://htseq.readthedocs.io/en/master/htseqcount.html](https://subread.sourceforge.net/featureCounts.html)) takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature. +[featureCounts](<[https://htseq.readthedocs.io/en/master/htseqcount.html](https://subread.sourceforge.net/featureCounts.html)>) takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature. [Kallisto](http://pachterlab.github.io/kallisto/) quantifies abundances of transcripts from RNA-Seq data using high-throughput sequencing reads. diff --git a/docs/usage.md b/docs/usage.md index 416effe..f0822bc 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -62,7 +62,6 @@ the following is a description of each field that can be used. Fields that do no | fastq_1 | `str` | `/path/to/*fastq.gz` | (none) | | fastq_2 | `str` | `/path/to/*fastq.gz` | (none) | - ### MAF Samplesheet You can optionally supply a secondary samplesheet with information for performing MAF fillouts, using the option `--maf_input`. Each row in this file requires a sample name that matches a sample name in the input samplesheet, and a path to relevant maf file. For example: From 6a9c24585f7a95ed58453f6e82b3bd0229f29f83 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc Date: Fri, 3 May 2024 11:16:11 -0400 Subject: [PATCH 14/39] prettier readme --- README.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/README.md b/README.md index 0653aec..121bbb0 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,6 @@ 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. - 3. Clone the pipeline repository and test it on a minimal dataset with the following steps: ```bash @@ -36,7 +35,6 @@ Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. - :::note If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) @@ -45,7 +43,6 @@ with `-profile test` before running the workflow on actual data. Now, you can run the pipeline using: - ```bash git clone git@github.com:mskcc/forte.git nextflow run forte/main.nf \ @@ -54,7 +51,6 @@ nextflow run forte/main.nf \ --outdir ``` - :::warning Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; From 64de02acbc783ca373cb29bf1cb70478b7df6d6c Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Fri, 3 May 2024 11:39:09 -0400 Subject: [PATCH 15/39] modify modules/local/metafusiongenebed bin --- .../resources/usr/bin/final_generate_v75_gene_bed.R | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R index 2d8c381..17caadc 100755 --- a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R +++ b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R @@ -16,12 +16,12 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") - message("final_generate_v75_gene_bed.R ") + message("final_generate_v75_gene_bed.R ") } args = commandArgs(TRUE) -if (length(args)!=3) { +if (length(args)!=2) { usage() quit() } @@ -37,13 +37,8 @@ gtf <- rtracklayer::import(args[1]) gtf_df <- as.data.frame(gtf) #remove incomplete transcripts mRNA_end_NF and mRNA_start_NF (not finished) gtf_df <- gtf_df[!grepl("NF",gtf_df$tag),] -#Add transcript version corresponding to gtf ensembl version -transcripts <- read.delim(args[2],header = F) -transcripts <- transcripts[,c("V15","V16")] -gtf_df <- merge(gtf_df, transcripts, by.x = "transcript_id",by.y = "V15") -gtf_df$transcript_id <- paste0(gtf_df$transcript_id,".",gtf_df$V16) -file.to_write <- args[3] +file.to_write <- args[2] gtf_df <- gtf_df %>% rename( From 1bcb4098b70046d0a62d92b27028fa479026909b Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 8 May 2024 10:49:11 -0400 Subject: [PATCH 16/39] add gff2bed step for metafusion genebed generation --- bin/final_generate_v75_gene_bed.R | 25 ++++++++++-------- modules/local/bedops/gff2bed/main.nf | 33 ++++++++++++++++++++++++ modules/local/metafusion/genebed/main.nf | 6 +++-- subworkflows/local/prepare_references.nf | 8 +++++- 4 files changed, 58 insertions(+), 14 deletions(-) create mode 100644 modules/local/bedops/gff2bed/main.nf diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index 17caadc..4c4f3a9 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -16,12 +16,12 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") - message("final_generate_v75_gene_bed.R ") + message("final_generate_v75_gene_bed.R ") } args = commandArgs(TRUE) -if (length(args)!=2) { +if (length(args)!=3) { usage() quit() } @@ -38,12 +38,15 @@ gtf_df <- as.data.frame(gtf) #remove incomplete transcripts mRNA_end_NF and mRNA_start_NF (not finished) gtf_df <- gtf_df[!grepl("NF",gtf_df$tag),] -file.to_write <- args[2] +total.introns.bed <- fread(file=args[2], header = FALSE, stringsAsFactors = F, sep="\t", na.strings = "",data.table = F) +colnames(total.introns.bed) <- c("chr","start","end","gene_id","tmp","strand","gene_biotype","type","V9","description") +total.introns.bed$transcript_id <- gsub("\\;.*","",str_split_fixed(total.introns.bed$description,"transcript_id=",n=2)[,2]) +total.introns.bed$gene_name <-gsub("\\;.*","",str_split_fixed(total.introns.bed$description,"gene_name=",n=2)[,2]) +total.introns.bed <- total.introns.bed[total.introns.bed$transcript_id %in% gtf_df$transcript_id,] -gtf_df <- gtf_df %>% - rename( - chr = seqnames - ) %>% +file.to_write <- args[3] + +total.introns.bed <- total.introns.bed %>% select(c(chr, start, end, transcript_id, type, strand, gene_name, gene_id)) %>% filter(type %in% c("exon","intron","UTR","CDS","cds","utr")) @@ -57,8 +60,8 @@ print(ptm) ## Forward strand: Exon 0 == Exon 1 ### Reverse strand: Exon 0 == LAST EXON IN TRANSCRIPT -print(dim(gtf_df)) -print(length(unique(gtf_df$transcript_id))) +print(dim(total.introns.bed)) +print(length(unique(total.introns.bed$transcript_id))) modify_transcript <- function(transcript){ @@ -122,11 +125,11 @@ modify_transcript <- function(transcript){ if(file.exists(file.to_write) ) {file.remove(file.to_write)} -gtf_df_modified <- gtf_df %>% +gtf_df_modified <- total.introns.bed %>% group_by(transcript_id,.drop = FALSE) %>% group_modify(~ modify_transcript(.x)) %>% select(c(chr, start, end, transcript_id, type, idx, strand, gene_name, gene_id )) %>% - arrange(chr,start,end) + arrange(chr,start,end, .by_group = T) time <- proc.time() - ptm print(time) diff --git a/modules/local/bedops/gff2bed/main.nf b/modules/local/bedops/gff2bed/main.nf new file mode 100644 index 0000000..d15dc99 --- /dev/null +++ b/modules/local/bedops/gff2bed/main.nf @@ -0,0 +1,33 @@ +process BEDOPS_GFF2BED { + tag "$meta.id" + label 'process_single' + + conda "bioconda::bedops=2.4.41" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedops:2.4.41--h9f5acd7_0' : + 'quay.io/biocontainers/bedops:2.4.41--h9f5acd7_0' }" + + input: + tuple val(meta), path(gff) + + output: + path('*.bed'), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + gff2bed \\ + $args \\ + < $gff > ${prefix}.introns.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedops: \$(bedops --version | awk '/version:/{print \$2}') + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 2314c40..0b709c2 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -8,7 +8,8 @@ process METAFUSION_GENEBED { 'quay.io/biocontainers/mulled-v2-28e4eeae4055c6901c8218fe9e55d342d59035ef:0b59d552b4c1c8b2845385236f1053a7e1fb80c6-0' }" input: - tuple val(meta), path(gff) + tuple val(meta), path(gtf) + path(bed) output: tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed @@ -22,7 +23,8 @@ process METAFUSION_GENEBED { def prefix = task.ext.prefix ?: "${meta.id}" """ final_generate_v75_gene_bed.R \\ - $gff \\ + $gtf \\ + $bed \\ ${prefix}.metafusion.gene.bed cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index 0040943..3b2ec95 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -16,6 +16,7 @@ include { ARRIBA_DOWNLOAD } from '../../modules/local/arriba/down include { KALLISTO_INDEX } from '../../modules/nf-core/kallisto/index/main' include { AGFUSION_DOWNLOAD } from '../../modules/local/agfusion/download/main' include { AGAT_SPADDINTRONS } from '../../modules/nf-core/agat/spaddintrons/main' +include { BEDOPS_GFF2BED } from '../../modules/local/bedops/gff2bed/main' include { METAFUSION_GENEBED } from '../../modules/local/metafusion/genebed/main' include { METAFUSION_GENEINFO } from '../../modules/local/metafusion/geneinfo/main' @@ -92,10 +93,15 @@ workflow PREPARE_REFERENCES { [] ) - METAFUSION_GENEBED( + BEDOPS_GFF2BED( AGAT_SPADDINTRONS.out.gff ) + METAFUSION_GENEBED( + [[:],gtf], + BEDOPS_GFF2BED.out.bed + ) + METAFUSION_GENEINFO( [[:],gtf], starfusion_ref,fusioncatcher_ref ) From 1264001641c0315bc96137036db730a5fff1a0d2 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc Date: Wed, 10 Jul 2024 14:21:33 -0400 Subject: [PATCH 17/39] revert use of BED, change gtf to 0 based start --- bin/final_generate_v75_gene_bed.R | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index 4c4f3a9..721cc82 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -16,12 +16,12 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") - message("final_generate_v75_gene_bed.R ") + message("final_generate_v75_gene_bed.R ") } args = commandArgs(TRUE) -if (length(args)!=3) { +if (length(args)!=2) { usage() quit() } @@ -38,17 +38,15 @@ gtf_df <- as.data.frame(gtf) #remove incomplete transcripts mRNA_end_NF and mRNA_start_NF (not finished) gtf_df <- gtf_df[!grepl("NF",gtf_df$tag),] -total.introns.bed <- fread(file=args[2], header = FALSE, stringsAsFactors = F, sep="\t", na.strings = "",data.table = F) -colnames(total.introns.bed) <- c("chr","start","end","gene_id","tmp","strand","gene_biotype","type","V9","description") -total.introns.bed$transcript_id <- gsub("\\;.*","",str_split_fixed(total.introns.bed$description,"transcript_id=",n=2)[,2]) -total.introns.bed$gene_name <-gsub("\\;.*","",str_split_fixed(total.introns.bed$description,"gene_name=",n=2)[,2]) -total.introns.bed <- total.introns.bed[total.introns.bed$transcript_id %in% gtf_df$transcript_id,] +file.to_write <- args[2] -file.to_write <- args[3] - -total.introns.bed <- total.introns.bed %>% +### convert start to 0-based to match metafusion expectations of gff format +gtf_df <- gtf_df %>% + rename( + chr = seqnames + ) %>% select(c(chr, start, end, transcript_id, type, strand, gene_name, gene_id)) %>% - filter(type %in% c("exon","intron","UTR","CDS","cds","utr")) + filter(type %in% c("exon","intron","UTR","CDS","cds","utr")) %>% mutate(start = start-1) #START CLOCK @@ -60,8 +58,8 @@ print(ptm) ## Forward strand: Exon 0 == Exon 1 ### Reverse strand: Exon 0 == LAST EXON IN TRANSCRIPT -print(dim(total.introns.bed)) -print(length(unique(total.introns.bed$transcript_id))) +print(dim(gtf_df)) +print(length(unique(gtf_df$transcript_id))) modify_transcript <- function(transcript){ @@ -125,11 +123,11 @@ modify_transcript <- function(transcript){ if(file.exists(file.to_write) ) {file.remove(file.to_write)} -gtf_df_modified <- total.introns.bed %>% +gtf_df_modified <- gtf_df %>% group_by(transcript_id,.drop = FALSE) %>% group_modify(~ modify_transcript(.x)) %>% select(c(chr, start, end, transcript_id, type, idx, strand, gene_name, gene_id )) %>% - arrange(chr,start,end, .by_group = T) + arrange(chr,start,end) time <- proc.time() - ptm print(time) @@ -141,4 +139,4 @@ write.table( quote=F, row.names=F, col.names=F -) +) \ No newline at end of file From f4b896ae4548e5c1d78bb34674d91db88794e264 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc Date: Wed, 10 Jul 2024 14:40:42 -0400 Subject: [PATCH 18/39] full revert of use of genebed in metafusion ref generation --- modules/local/bedops/gff2bed/main.nf | 33 ------------------------ modules/local/metafusion/genebed/main.nf | 2 -- subworkflows/local/prepare_references.nf | 8 +----- 3 files changed, 1 insertion(+), 42 deletions(-) delete mode 100644 modules/local/bedops/gff2bed/main.nf diff --git a/modules/local/bedops/gff2bed/main.nf b/modules/local/bedops/gff2bed/main.nf deleted file mode 100644 index d15dc99..0000000 --- a/modules/local/bedops/gff2bed/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -process BEDOPS_GFF2BED { - tag "$meta.id" - label 'process_single' - - conda "bioconda::bedops=2.4.41" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedops:2.4.41--h9f5acd7_0' : - 'quay.io/biocontainers/bedops:2.4.41--h9f5acd7_0' }" - - input: - tuple val(meta), path(gff) - - output: - path('*.bed'), emit: bed - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - gff2bed \\ - $args \\ - < $gff > ${prefix}.introns.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedops: \$(bedops --version | awk '/version:/{print \$2}') - END_VERSIONS - """ -} \ No newline at end of file diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 0b709c2..2fc99bd 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -9,7 +9,6 @@ process METAFUSION_GENEBED { input: tuple val(meta), path(gtf) - path(bed) output: tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed @@ -24,7 +23,6 @@ process METAFUSION_GENEBED { """ final_generate_v75_gene_bed.R \\ $gtf \\ - $bed \\ ${prefix}.metafusion.gene.bed cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index 3b2ec95..82a2f99 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -16,7 +16,6 @@ include { ARRIBA_DOWNLOAD } from '../../modules/local/arriba/down include { KALLISTO_INDEX } from '../../modules/nf-core/kallisto/index/main' include { AGFUSION_DOWNLOAD } from '../../modules/local/agfusion/download/main' include { AGAT_SPADDINTRONS } from '../../modules/nf-core/agat/spaddintrons/main' -include { BEDOPS_GFF2BED } from '../../modules/local/bedops/gff2bed/main' include { METAFUSION_GENEBED } from '../../modules/local/metafusion/genebed/main' include { METAFUSION_GENEINFO } from '../../modules/local/metafusion/geneinfo/main' @@ -93,13 +92,8 @@ workflow PREPARE_REFERENCES { [] ) - BEDOPS_GFF2BED( - AGAT_SPADDINTRONS.out.gff - ) - METAFUSION_GENEBED( - [[:],gtf], - BEDOPS_GFF2BED.out.bed + AGAT_SPADDINTRONS.out.gff ) METAFUSION_GENEINFO( From 9cb8943740bcb47f8eb3ded208edbe35de2cfce7 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 10 Jul 2024 14:46:39 -0400 Subject: [PATCH 19/39] gtf should be gff to match previous --- modules/local/metafusion/genebed/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 2fc99bd..2314c40 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -8,7 +8,7 @@ process METAFUSION_GENEBED { 'quay.io/biocontainers/mulled-v2-28e4eeae4055c6901c8218fe9e55d342d59035ef:0b59d552b4c1c8b2845385236f1053a7e1fb80c6-0' }" input: - tuple val(meta), path(gtf) + tuple val(meta), path(gff) output: tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed @@ -22,7 +22,7 @@ process METAFUSION_GENEBED { def prefix = task.ext.prefix ?: "${meta.id}" """ final_generate_v75_gene_bed.R \\ - $gtf \\ + $gff \\ ${prefix}.metafusion.gene.bed cat <<-END_VERSIONS > versions.yml From 35f1f789adca0a87c8f7e9a26177a5090d1340f1 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Mon, 16 Sep 2024 13:41:43 -0400 Subject: [PATCH 20/39] Rename clinical file, update metafusion docker --- .../{clinical_whitelist.txt => clinical_allowlist_hg19.txt} | 0 conf/igenomes.config | 2 +- modules/local/metafusion/container/Dockerfile | 4 ++-- 3 files changed, 3 insertions(+), 3 deletions(-) rename assets/{clinical_whitelist.txt => clinical_allowlist_hg19.txt} (100%) diff --git a/assets/clinical_whitelist.txt b/assets/clinical_allowlist_hg19.txt similarity index 100% rename from assets/clinical_whitelist.txt rename to assets/clinical_allowlist_hg19.txt diff --git a/conf/igenomes.config b/conf/igenomes.config index 81770ab..043bfe4 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -31,7 +31,7 @@ params { } } metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" - clinicalgenes = "${projectDir}/assets/clinical_whitelist.txt" + clinicalgenes = "${projectDir}/assets/clinical_allowlist_hg19.txt" ensembl_version = 75 transcripts = "https://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_core_75_37/transcript.txt.gz" } diff --git a/modules/local/metafusion/container/Dockerfile b/modules/local/metafusion/container/Dockerfile index a2bd7f1..9b55238 100755 --- a/modules/local/metafusion/container/Dockerfile +++ b/modules/local/metafusion/container/Dockerfile @@ -2,9 +2,9 @@ FROM mapostolides/metafusion:latest LABEL author="Alexandria Dymun (pintoa1@mskcc.org)" \ maintainer="Anne Marie Noronha (noronhaa@mskcc.org)" \ - version.image="0.0.6" + version.image="0.0.8" -ENV METAFUSION_TAG="v1.0.2" +ENV METAFUSION_TAG="v1.0.3" ENV PATH="${PATH}:/MetaFusion/scripts" RUN R -e "chooseCRANmirror(ind=52); install.packages(c('plyr','data.table'))" From b21585215770c40505ba8cf88b195881af52238b Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Mon, 16 Sep 2024 14:02:41 -0400 Subject: [PATCH 21/39] New version of metafusion_forte.sh --- bin/Metafusion_forte.sh | 4 ++-- modules/local/metafusion/run/main.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bin/Metafusion_forte.sh b/bin/Metafusion_forte.sh index 404328d..470df60 100755 --- a/bin/Metafusion_forte.sh +++ b/bin/Metafusion_forte.sh @@ -7,7 +7,7 @@ set -eo pipefail # __author__ = "Alexandria Dymun" # __email__ = "pintoa1@mskcc.org" # __contributor__ = "Anne Marie Noronha (noronhaa@mskcc.org)" -# __version__ = "0.0.1" +# __version__ = "0.0.2" # __status__ = "Dev" output_ANC_RT_SG=1 @@ -15,7 +15,7 @@ RT_call_filter=1 blck_filter=1 ANC_filter=1 usage() { - echo "Usage: Metafusion_forte.sh --num_tools= --genome_fasta --recurrent_bedpe --outdir --cff --gene_bed --gene_info " 1>&2; + echo "Usage: Metafusion_forte.sh --num_tools= --genome_fasta --recurrent_bedpe --outdir --cff --gene_bed --gene_info --clinical_genes " 1>&2; exit 1; } diff --git a/modules/local/metafusion/run/main.nf b/modules/local/metafusion/run/main.nf index 4aa21c3..19e4b2b 100644 --- a/modules/local/metafusion/run/main.nf +++ b/modules/local/metafusion/run/main.nf @@ -44,7 +44,7 @@ process METAFUSION_RUN { cat <<-END_VERSIONS > versions.yml "${task.process}": Metafusion docker: \$METAFUSION_TAG - Metafusion_forte.sh: 0.0.1 + Metafusion_forte.sh: 0.0.2 END_VERSIONS """ } From d906a0cbabecb6daa25890b6e8dcfd7739e41116 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Mon, 16 Sep 2024 14:25:11 -0400 Subject: [PATCH 22/39] remove terra designation, change metafusion docker version --- bin/final_generate_v75_gene_bed.R | 2 +- conf/terra.config | 63 ------------------- .../usr/bin/final_generate_v75_gene_bed.R | 2 +- modules/local/metafusion/run/main.nf | 4 +- nextflow.config | 1 - 5 files changed, 4 insertions(+), 68 deletions(-) delete mode 100644 conf/terra.config diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index 721cc82..425d4f7 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -8,7 +8,7 @@ suppressPackageStartupMessages({ -# library(plyr) + library(plyr) library(dplyr) library(data.table) library(stringr) diff --git a/conf/terra.config b/conf/terra.config deleted file mode 100644 index 643cd7b..0000000 --- a/conf/terra.config +++ /dev/null @@ -1,63 +0,0 @@ -executor { - name = "lsf" - queueSize = 5000000000 - perJobMemLimit = true -} - -process { - memory = "8.GB" - time = { 3.h * task.attempt } - clusterOptions = "" - scratch = true - beforeScript = "module load singularity/3.1.1; unset R_LIBS; catch_term () { echo 'caught USR2/TERM signal'; set +e; false; on_exit ; } ; trap catch_term USR2 TERM" - errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' } - maxRetries = 3 - - withLabel:process_single { - cpus = { check_max( 1, 'cpus' ) } - memory = { round_memory( check_max( 8.GB * task.cpus * task.attempt, 'memory' )/task.cpus, "down") } - time = { check_max( 4.h * task.attempt, 'time' ) } - } - withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } - time = { check_max( 4.h * task.attempt, 'time' ) } - } - withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } - time = { check_max( 8.h * task.attempt, 'time' ) } - } - withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { round_memory( check_max( 8.GB * task.cpus, 'memory' )/task.cpus, "down") } - time = { check_max( 16.h * task.attempt, 'time' ) } - } - withLabel:process_high_memory { - memory = { round_memory( check_max( 200.GB * task.cpus, 'memory' )/task.cpus, "down") } - } - withLabel:process_low { - time = { check_max( 50.h * task.attempt, 'time' ) } - } -} - -params { - max_memory = "128.GB" - max_cpus = 24 - max_time = "500.h" - mem_per_core = true - reference_base = "/juno/work/ccs/cmopipeline/forte" - igenomes_base = '/juno/cmo/tempo/cmopipeline/mskcc-igenomes/igenomes' - targets_base = '/juno/work/ccs/cmopipeline/forte' -} - -env { - SPARK_LOCAL_DIRS = './' -} - -singularity { - enabled = true - runOptions = "-B $TMPDIR" - autoMounts = true - cacheDir = "/juno/cmo/tempo/cmopipeline/singularity_images/" -} diff --git a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R index 17caadc..0f21082 100755 --- a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R +++ b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R @@ -8,7 +8,7 @@ suppressPackageStartupMessages({ -# library(plyr) + library(plyr) library(dplyr) library(data.table) library(stringr) diff --git a/modules/local/metafusion/run/main.nf b/modules/local/metafusion/run/main.nf index 19e4b2b..42e251c 100644 --- a/modules/local/metafusion/run/main.nf +++ b/modules/local/metafusion/run/main.nf @@ -3,8 +3,8 @@ process METAFUSION_RUN { label "process_low" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker://cmopipeline/metafusion:0.0.7' : - 'docker.io/cmopipeline/metafusion:0.0.7' }" + 'docker://cmopipeline/metafusion:0.0.8' : + 'docker.io/cmopipeline/metafusion:0.0.8' }" input: tuple val(meta), path(cff) diff --git a/nextflow.config b/nextflow.config index a174366..15448bf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -198,7 +198,6 @@ profiles { } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } - terra { includeConfig 'conf/terra.config' } juno { includeConfig 'conf/juno.config' } } From 6823a2448525ac3b34d239a45060c393a5ae7dd1 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 18 Sep 2024 11:02:34 -0400 Subject: [PATCH 23/39] Fix NA values in final CFF --- bin/add_annotations_cff.R | 2 +- bin/add_flags_and_cluster_information.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/add_annotations_cff.R b/bin/add_annotations_cff.R index 97ceb57..fa27a3e 100755 --- a/bin/add_annotations_cff.R +++ b/bin/add_annotations_cff.R @@ -107,7 +107,7 @@ cff <- merge( all.x = T, all.y = F) -cff$gene5_transcript_id <- paste0(cff$gene5_transcript_id,".",cff$V16) +cff$gene5_transcript_id <- ifelse(is.na(cff$gene5_transcript_id),NA,paste0(cff$gene5_transcript_id,".",cff$V16)) cff$V16 <- NULL cff <- as.data.frame(cff)[,c(final_cff_cols)] diff --git a/bin/add_flags_and_cluster_information.R b/bin/add_flags_and_cluster_information.R index 0482a79..6b0c6a4 100755 --- a/bin/add_flags_and_cluster_information.R +++ b/bin/add_flags_and_cluster_information.R @@ -186,7 +186,7 @@ library(data.table) ) if (!is.null(filters)){ unfiltered_cff <- merge(unfiltered_cff,filters, by="FID", all.x = T, all.y = F) %>% - mutate(Metafusion_flag=ifelse(is.null(Metafusion_flag) | is.na(Metafusion_flag) | Metafusion_flag=="", tmpflag, paste(Metafusion_flag,tmpflag,sep=","))) %>% + mutate(Metafusion_flag=ifelse(is.null(Metafusion_flag) | is.na(Metafusion_flag) | Metafusion_flag=="", tmpflag, ifelse(!is.na(tmpflag), Metafusion_flag, paste(Metafusion_flag,tmpflag,sep=",")))) %>% select(-c(tmpflag)) } From dba6361da5e425129abf339e3fa2f3530e2ec597 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 18 Sep 2024 12:05:50 -0400 Subject: [PATCH 24/39] Clean up flagging and versions of transcripts --- bin/add_annotations_cff.R | 2 +- bin/add_flags_and_cluster_information.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/add_annotations_cff.R b/bin/add_annotations_cff.R index fa27a3e..bf22a75 100755 --- a/bin/add_annotations_cff.R +++ b/bin/add_annotations_cff.R @@ -97,7 +97,7 @@ cff <- merge( by.y = "V15", all.x = T , all.y = F) -cff$gene3_transcript_id <- paste0(cff$gene3_transcript_id,".",cff$V16) +cff$gene3_transcript_id <- ifelse(is.na(cff$gene3_transcript_id),NA,paste0(cff$gene3_transcript_id,".",cff$V16)) cff$V16 <- NULL cff <- merge( cff, diff --git a/bin/add_flags_and_cluster_information.R b/bin/add_flags_and_cluster_information.R index 6b0c6a4..6d4d354 100755 --- a/bin/add_flags_and_cluster_information.R +++ b/bin/add_flags_and_cluster_information.R @@ -186,7 +186,7 @@ library(data.table) ) if (!is.null(filters)){ unfiltered_cff <- merge(unfiltered_cff,filters, by="FID", all.x = T, all.y = F) %>% - mutate(Metafusion_flag=ifelse(is.null(Metafusion_flag) | is.na(Metafusion_flag) | Metafusion_flag=="", tmpflag, ifelse(!is.na(tmpflag), Metafusion_flag, paste(Metafusion_flag,tmpflag,sep=",")))) %>% + mutate(Metafusion_flag=ifelse(is.null(Metafusion_flag) | is.na(Metafusion_flag) | Metafusion_flag=="", tmpflag, ifelse(is.na(tmpflag), Metafusion_flag, paste(Metafusion_flag,tmpflag,sep=",")))) %>% select(-c(tmpflag)) } From 4f3fbbbcaf69e228cb1ecf149d25fade9ca8d90b Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 18 Sep 2024 12:25:44 -0400 Subject: [PATCH 25/39] update version of generate gene bed --- bin/final_generate_v75_gene_bed.R | 2 +- modules/local/metafusion/genebed/main.nf | 4 ++-- .../genebed/resources/usr/bin/final_generate_v75_gene_bed.R | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index 425d4f7..0ea0055 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -3,7 +3,7 @@ # __author__ = "Alexandria Dymun" # __email__ = "pintoa1@mskcc.org" # __contributor__ = "Anne Marie Noronha (noronhaa@mskcc.org)" -# __version__ = "0.0.1" +# __version__ = "0.0.2" # __status__ = "Dev" diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 2314c40..1936846 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -28,7 +28,7 @@ process METAFUSION_GENEBED { cat <<-END_VERSIONS > versions.yml "${task.process}": R: \$(R --version | head -n1) - final_generate_v75_gene_bed.R: 0.0.1 + final_generate_v75_gene_bed.R: 0.0.2 END_VERSIONS """ @@ -41,7 +41,7 @@ process METAFUSION_GENEBED { cat <<-END_VERSIONS > versions.yml "${task.process}": R: \$(R --version | head -n1) - final_generate_v75_gene_bed.R: 0.0.1 + final_generate_v75_gene_bed.R: 0.0.2 END_VERSIONS """ } diff --git a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R index 0f21082..4d92058 100755 --- a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R +++ b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R @@ -3,7 +3,7 @@ # __author__ = "Alexandria Dymun" # __email__ = "pintoa1@mskcc.org" # __contributor__ = "Anne Marie Noronha (noronhaa@mskcc.org)" -# __version__ = "0.0.1" +# __version__ = "0.0.2" # __status__ = "Dev" From ec110ca2f702da38b7bec0a9b9c03df6f1608d38 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 18 Sep 2024 14:15:04 -0400 Subject: [PATCH 26/39] Remove scientific formatting in genebed --- bin/final_generate_v75_gene_bed.R | 1 + .../genebed/resources/usr/bin/final_generate_v75_gene_bed.R | 1 + 2 files changed, 2 insertions(+) diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index 0ea0055..aedb4a1 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -12,6 +12,7 @@ suppressPackageStartupMessages({ library(dplyr) library(data.table) library(stringr) + options(scipen = 999) }) usage <- function() { diff --git a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R index 3b114b6..4e5191c 100755 --- a/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R +++ b/modules/local/metafusion/genebed/resources/usr/bin/final_generate_v75_gene_bed.R @@ -12,6 +12,7 @@ suppressPackageStartupMessages({ library(dplyr) library(data.table) library(stringr) + options(scipen = 999) }) usage <- function() { From 0d0c065c81d45468c527002933e9131df3e6be66 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Wed, 18 Sep 2024 14:26:29 -0400 Subject: [PATCH 27/39] Update output.md --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 210cd96..3a5c61e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -141,7 +141,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d -FORTE uses a custom fork of [Metafusion](https://github.com/mskcc/MetaFusion) to filter, cluster and annotate the fusion calls. Several `intermediate` files are included in the output. +FORTE uses a custom fork of [Metafusion](https://github.com/mskcc/MetaFusion) to filter, cluster and annotate the fusion calls. Several `intermediate` files are included in the output, [see wiki for detailed information](https://github.com/mskcc/forte/wiki/Metafusion-Output). `Fusion_effect` information is added using a custom fork of [AGFusion](https://github.com/anoronh4/AGFusion). From c294e0608a984f1f5b6cf552ecf681ac7ce19221 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Wed, 18 Sep 2024 14:29:36 -0400 Subject: [PATCH 28/39] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8985042..e54838a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,12 +10,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#117](https://github.com/mskcc/forte/pull/117) - add supporting-reads_gene-fusions\*.zip files to fusioncatcher outputs - [#118](https://github.com/mskcc/forte/pull/118) - change the way the plug-n-play starfusion reference is downloaded. +- -[#126](https://github.com/mskcc/forte/pull/126) - enable clinical genes prioritization in Metafusion ### `Fixed` - [#119](https://github.com/mskcc/forte/pull/119) - change script error behavior in METAFUSION_RUN process - [#125](https://github.com/mskcc/forte/pull/125) - update upload-artifact version because the version previously in use (v2) is deprecated. +- [#126](https://github.com/mskcc/forte/pull/126) - 0 based gene bed annotation with removal of incomplete transcripts ### `Dependencies` From 2486a60ff6ae99cf1684b681c998844e38ef4362 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 18 Sep 2024 14:37:13 -0400 Subject: [PATCH 29/39] fix linting --- bin/final_generate_v75_gene_bed.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/final_generate_v75_gene_bed.R b/bin/final_generate_v75_gene_bed.R index aedb4a1..406f013 100755 --- a/bin/final_generate_v75_gene_bed.R +++ b/bin/final_generate_v75_gene_bed.R @@ -140,4 +140,4 @@ write.table( quote=F, row.names=F, col.names=F -) \ No newline at end of file +) From cf665a66c99aa0f700d6877ed3239fa1817726b2 Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Mon, 23 Sep 2024 09:43:14 -0400 Subject: [PATCH 30/39] Update igenomes.config --- conf/igenomes.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 043bfe4..41d857c 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -50,7 +50,7 @@ params { cdna = "http://ftp.ensemblgenomes.org/pub/viruses/fasta/sars_cov_2/cdna/Sars_cov_2.ASM985889v3.cdna.all.fa.gz" metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37_test/blocklist_breakpoints.bedpe" ensembl_version = 75 - clinicalgenes = "${projectDir}/assets/clinical_whitelist.txt" + clinicalgenes = "${projectDir}/assets/clinical_allowlist_hg19.txt" transcripts = "https://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_core_75_37/transcript.txt.gz" } /* From 0bb2044afda639489ff9ff9a1080c6fb9183908a Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Mon, 23 Sep 2024 09:44:05 -0400 Subject: [PATCH 31/39] Update fusion.nf --- subworkflows/local/fusion.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf index 6b2f2f5..5d4dcf9 100644 --- a/subworkflows/local/fusion.nf +++ b/subworkflows/local/fusion.nf @@ -142,7 +142,7 @@ workflow FUSION { ADD_FLAG.out.unfiltered_cff .join(ONCOKB_FUSIONANNOTATOR.out.oncokb_fusions, by:0) .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0), - transcipts + transcripts ) } else { CFF_FINALIZE( From 8cff61f94ad98866132795df700ccacf451f02a7 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Mon, 23 Sep 2024 11:38:30 -0400 Subject: [PATCH 32/39] Match nfcore standards for id of genebed --- modules/local/metafusion/genebed/main.nf | 3 +-- subworkflows/local/prepare_references.nf | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 27a1a7f..1936846 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -9,7 +9,6 @@ process METAFUSION_GENEBED { input: tuple val(meta), path(gff) - val ensembl_version output: tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed @@ -24,7 +23,7 @@ process METAFUSION_GENEBED { """ final_generate_v75_gene_bed.R \\ $gff \\ - ${ensembl_version}.metafusion.gene.bed + ${prefix}.metafusion.gene.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index 735cb80..caaed87 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -88,13 +88,12 @@ workflow PREPARE_REFERENCES { //cosmic_passwd = params.cosmic_passwd ?: "" AGAT_SPADDINTRONS( - [[:],gtf], + [[id:params.ensembl_version],gtf], [] ) METAFUSION_GENEBED( - AGAT_SPADDINTRONS.out.gff, - params.ensembl_version + AGAT_SPADDINTRONS.out.gff ) METAFUSION_GENEINFO( From 5ec1d7eb49b74f2dcc31bbd59e9f05c63e92a894 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Mon, 23 Sep 2024 11:44:28 -0400 Subject: [PATCH 33/39] Ensure nextflow checks for correct version of ensembl gene bed file, not just any gene bed file --- modules/local/metafusion/genebed/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf index 1936846..97b4d12 100644 --- a/modules/local/metafusion/genebed/main.nf +++ b/modules/local/metafusion/genebed/main.nf @@ -11,7 +11,7 @@ process METAFUSION_GENEBED { tuple val(meta), path(gff) output: - tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed + tuple val(meta), path("${meta.id}.metafusion.gene.bed"), emit: metafusion_gene_bed path "versions.yml" , emit: versions when: From bf4e6be2bc3265efb24a7cb3350e54edc6a8f439 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Mon, 23 Sep 2024 15:31:09 -0400 Subject: [PATCH 34/39] allow for more memory in AGAT --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index 9277358..aa63a22 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -210,6 +210,7 @@ process { ] } withName: 'AGAT_SPADDINTRONS' { + cpus = 4 storeDir = { "${params.reference_base}/${params.genome}/metafusion/introns" } publishDir = [ enabled: false, From 6ef6e33e2f4f48d7b0609e05922ff7dfece6c87b Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Thu, 10 Oct 2024 11:21:41 -0400 Subject: [PATCH 35/39] Update CHANGELOG.md --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 30ec6f5..204f02c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#119](https://github.com/mskcc/forte/pull/119) - change script error behavior in METAFUSION_RUN process - [#125](https://github.com/mskcc/forte/pull/125) - update upload-artifact version because the version previously in use (v2) is deprecated. -- [#126](https://github.com/mskcc/forte/pull/126) - 0 based gene bed annotation with removal of incomplete transcripts - [#124](https://github.com/mskcc/forte/pull/124) - ensure genebed file as 0based start site From fe869198bb5e639745f1a0de2cdd7e5a658d94a2 Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 6 Nov 2024 16:13:44 -0500 Subject: [PATCH 36/39] Remove transcripts file for versions, update allowlist to include all mane transcripts --- CHANGELOG.md | 2 +- assets/mane_v1.2_allowlist.txt | 19317 +++++++++++++++++++++ bin/add_annotations_cff.R | 31 +- conf/igenomes.config | 2 +- modules/local/cff_annotate/main.nf | 4 +- subworkflows/local/fusion.nf | 6 +- subworkflows/local/prepare_references.nf | 2 +- 7 files changed, 19327 insertions(+), 37 deletions(-) create mode 100644 assets/mane_v1.2_allowlist.txt diff --git a/CHANGELOG.md b/CHANGELOG.md index efb5ab3..b0c5bde 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#117](https://github.com/mskcc/forte/pull/117) - add supporting-reads_gene-fusions\*.zip files to fusioncatcher outputs - [#118](https://github.com/mskcc/forte/pull/118) - change the way the plug-n-play starfusion reference is downloaded. -- -[#126](https://github.com/mskcc/forte/pull/126) - enable clinical genes prioritization in Metafusion +- [#126](https://github.com/mskcc/forte/pull/126) - enable clinical genes prioritization in Metafusion - [#128](https://github.com/mskcc/forte/pull/128) - full support for GRCh38 added diff --git a/assets/mane_v1.2_allowlist.txt b/assets/mane_v1.2_allowlist.txt new file mode 100644 index 0000000..a89f53e --- /dev/null +++ b/assets/mane_v1.2_allowlist.txt @@ -0,0 +1,19317 @@ +gene_name ensembl_transcript refseq_transcript +PRDM16 ENST00000270722 NM_022114.4 +PEX10 ENST00000447513 NM_002617.4 +PEX14 ENST00000356607 NM_004565.3 +PLCH2 ENST00000378486 NM_014638.4 +SPSB1 ENST00000328089 NM_025106.4 +SLC2A5 ENST00000377424 NM_003039.3 +NMNAT1 ENST00000377205 NM_022787.4 +DISP3 ENST00000294484 NM_020780.2 +MMEL1 ENST00000378412 NM_033467.4 +TMEM51 ENST00000376008 NM_001136218.2 +FBXO42 ENST00000375592 NM_018994.3 +ALDH4A1 ENST00000375341 NM_003748.4 +RER1 ENST00000605895 NM_007033.5 +PANK4 ENST00000378466 NM_018216.4 +VPS13D ENST00000620676 NM_015378.4 +RBP7 ENST00000294435 NM_052960.3 +GPR157 ENST00000377411 NM_024980.5 +ZBTB40 ENST00000375647 NM_014870.4 +NPHP4 ENST00000378156 NM_015102.5 +HES5 ENST00000378453 NM_001010926.4 +SZRD1 ENST00000401088 NM_001114600.3 +PHACTR4 ENST00000373839 NM_001048183.3 +SLC9A1 ENST00000263980 NM_003047.5 +LDLRAP1 ENST00000374338 NM_015627.3 +PAFAH2 ENST00000374282 NM_000437.4 +AJAP1 ENST00000378191 NM_018836.4 +PTAFR ENST00000373857 NM_000952.5 +SLC25A33 ENST00000302692 NM_032315.3 +GJB3 ENST00000373366 NM_024009.3 +EYA3 ENST00000373871 NM_001990.4 +EPHA2 ENST00000358432 NM_004431.5 +ARHGEF19 ENST00000270747 NM_153213.5 +KAZN ENST00000376030 NM_201628.3 +TNFRSF1B ENST00000376259 NM_001066.3 +UBE4B ENST00000343090 NM_001105562.3 +PLA2G5 ENST00000375108 NM_000929.3 +PTPRU ENST00000373779 NM_133178.4 +ZMYM6 ENST00000357182 NM_007167.4 +GJB5 ENST00000338513 NM_005268.4 +AGO4 ENST00000373210 NM_017629.4 +CPLANE2 ENST00000375599 NM_030907.4 +ZBTB8B ENST00000609129 NM_001145720.2 +PAX7 ENST00000420770 NM_001135254.2 +CASZ1 ENST00000377022 NM_001079843.3 +DNALI1 ENST00000652629 NM_003462.5 +RRAGC ENST00000373001 NM_022157.4 +GRIK3 ENST00000373091 NM_000831.4 +PLA2G2D ENST00000375105 NM_012400.4 +GUCA2B ENST00000372581 NM_007102.3 +RCC2 ENST00000375436 NM_018715.4 +PSMB2 ENST00000373237 NM_002794.5 +THRAP3 ENST00000354618 NM_005119.4 +PADI6 ENST00000619609 NM_207421.4 +PADI4 ENST00000375448 NM_012387.3 +RHBDL2 ENST00000372990 NM_017821.5 +CFAP144 ENST00000335282 NM_001101376.3 +ZMYM4 ENST00000314607 NM_005095.3 +C1orf216 ENST00000270815 NM_152374.2 +ACTL8 ENST00000375406 NM_030812.3 +RLF ENST00000372771 NM_012421.4 +CLSPN ENST00000318121 NM_022111.4 +GNL2 ENST00000373062 NM_013285.3 +GJA4 ENST00000342280 NM_002060.3 +MORN1 ENST00000378531 NM_024848.3 +TTC22 ENST00000371276 NM_001114108.2 +TIE1 ENST00000372476 NM_005424.5 +MYCBP ENST00000397572 NM_012333.5 +DLGAP3 ENST00000373347 NM_001080418.3 +RIMS3 ENST00000372684 NM_014747.3 +RAB3B ENST00000371655 NM_002867.4 +SMIM12 ENST00000521580 NM_138428.6 +CZIB ENST00000294360 NM_017887.3 +FAM151A ENST00000302250 NM_176782.3 +OSBPL9 ENST00000428468 NM_024586.6 +C1orf210 ENST00000523677 NM_182517.3 +PARS2 ENST00000371279 NM_152268.4 +ZYG11B ENST00000294353 NM_024646.3 +L1TD1 ENST00000498273 NM_019079.5 +TXNDC12 ENST00000371626 NM_015913.4 +TTC4 ENST00000371281 NM_004623.5 +KLF17 ENST00000372299 NM_173484.4 +PLPP3 ENST00000371250 NM_003713.5 +SNIP1 ENST00000296215 NM_024700.4 +CPT2 ENST00000371486 NM_000098.3 +FOXJ3 ENST00000361346 NM_014947.5 +TUT4 ENST00000257177 NM_001009881.3 +KLF18 ENST00000634670 NM_001358438.1 +MAGOH ENST00000371470 NM_002370.4 +CDKN2C ENST00000371761 NM_078626.3 +C1orf87 ENST00000371201 NM_152377.3 +ZSWIM5 ENST00000359600 NM_020883.2 +OMA1 ENST00000371226 NM_145243.5 +SLC35D1 ENST00000235345 NM_015139.3 +LRP8 ENST00000306052 NM_004631.5 +TCEANC2 ENST00000234827 NM_153035.3 +KTI12 ENST00000371614 NM_138417.3 +KANK4 ENST00000371153 NM_181712.5 +USP1 ENST00000339950 NM_003368.5 +AK5 ENST00000354567 NM_174858.3 +GIPC2 ENST00000370759 NM_017655.6 +RPE65 ENST00000262340 NM_000329.3 +ANGPTL3 ENST00000371129 NM_014495.4 +DNAJC6 ENST00000371069 NM_001256864.2 +AK4 ENST00000327299 NM_013410.4 +LEPROT ENST00000371065 NM_017526.5 +CACHD1 ENST00000651257 NM_020925.4 +EFCAB7 ENST00000371088 NM_032437.4 +MCOLN2 ENST00000370608 NM_153259.4 +ST6GALNAC5 ENST00000477717 NM_030965.3 +ATG4C ENST00000317868 NM_032852.4 +ADGRL4 ENST00000370742 NM_022159.4 +GJA9 ENST00000357771 NM_030772.5 +TTLL7 ENST00000260505 NM_024686.6 +KDM4A ENST00000372396 NM_014663.3 +ZNHIT6 ENST00000370574 NM_017953.4 +MROH7 ENST00000421030 NM_001039464.4 +PTGFR ENST00000370757 NM_000959.4 +LMO4 ENST00000370544 NM_006769.4 +PRPF38A ENST00000257181 NM_032864.4 +PIGK ENST00000370812 NM_005482.3 +GUCA2A ENST00000357001 NM_033553.3 +DOCK7 ENST00000635253 NM_001367561.1 +NEGR1 ENST00000357731 NM_173808.3 +KYAT3 ENST00000260508 NM_001008661.3 +SHISAL2A ENST00000517870 NM_001042693.3 +DNTTIP2 ENST00000436063 NM_014597.5 +PTPRF ENST00000359947 NM_002840.5 +DHCR24 ENST00000371269 NM_014762.4 +COL24A1 ENST00000370571 NM_152890.7 +GPX7 ENST00000361314 NM_015696.5 +SLC44A3 ENST00000271227 NM_001114106.3 +PKN2 ENST00000370521 NM_006256.4 +ABCD3 ENST00000370214 NM_002858.4 +ALG14 ENST00000370205 NM_144988.4 +ZZZ3 ENST00000370801 NM_015534.6 +GJB4 ENST00000339480 NM_153212.3 +TMEM125 ENST00000439858 NM_144626.3 +DMRTA2 ENST00000404795 NM_032110.3 +HIVEP3 ENST00000372583 NM_024503.5 +BCAR3 ENST00000260502 NM_003567.4 +BARHL2 ENST00000370445 NM_020063.2 +CNN3 ENST00000370206 NM_001839.5 +VAV3 ENST00000370056 NM_006113.5 +DPYD ENST00000370192 NM_000110.4 +TLCD4 ENST00000370203 NM_152487.3 +LRRC8D ENST00000337338 NM_001134479.2 +S1PR1 ENST00000305352 NM_001400.5 +ELAPOR1 ENST00000369939 NM_020775.5 +ARHGAP29 ENST00000260526 NM_004815.4 +PGM1 ENST00000371084 NM_002633.3 +IGSF21 ENST00000251296 NM_032880.5 +COA7 ENST00000371538 NM_023077.3 +OLFML3 ENST00000320334 NM_020190.5 +GCLM ENST00000370238 NM_002061.4 +TGFBR3 ENST00000212355 NM_003243.5 +SZT2 ENST00000634258 NM_001365999.1 +PHTF1 ENST00000369604 NM_001323043.2 +F3 ENST00000334047 NM_001993.5 +VCAM1 ENST00000294728 NM_001078.4 +GPR88 ENST00000315033 NM_022049.3 +RWDD3 ENST00000370202 NM_015485.5 +MAN1A2 ENST00000356554 NM_006699.5 +LPAR3 ENST00000370611 NM_012152.3 +CTTNBP2NL ENST00000271277 NM_018704.3 +CIMAP3 ENST00000369738 NM_181643.6 +TSPAN2 ENST00000369516 NM_005725.6 +LRIG2 ENST00000361127 NM_014813.3 +SLC35A3 ENST00000533028 NM_012243.3 +AGL ENST00000361915 NM_000642.3 +SLC6A17 ENST00000331565 NM_001010898.4 +HSD3B2 ENST00000369416 NM_000198.4 +RNPC3 ENST00000423855 NM_017619.4 +SNX7 ENST00000306121 NM_015976.5 +SLC30A7 ENST00000357650 NM_133496.5 +SEC22B ENST00000578049 NM_004892.6 +PTGFRN ENST00000393203 NM_020440.4 +ZNF326 ENST00000340281 NM_182976.4 +TRIM45 ENST00000256649 NM_025188.4 +TENT5C ENST00000369448 NM_017709.4 +SYCP1 ENST00000369522 NM_003176.4 +PIP5K1A ENST00000368888 NM_001135638.2 +GDAP2 ENST00000369443 NM_017686.4 +TSHB ENST00000256592 NM_000549.5 +WDR3 ENST00000349139 NM_006784.3 +SLC22A15 ENST00000369503 NM_018420.3 +SCNM1 ENST00000368905 NM_024041.4 +FLG ENST00000368799 NM_002016.2 +CDC14A ENST00000336454 NM_003672.4 +CD53 ENST00000271324 NM_000560.4 +FLG2 ENST00000388718 NM_001014342.3 +SRGAP2C ENST00000367123 NM_001329984.2 +SPAG17 ENST00000336338 NM_206996.4 +TTF2 ENST00000369466 NM_003594.4 +MAGI3 ENST00000307546 NM_001142782.2 +GABPB2 ENST00000368918 NM_144618.3 +CD5L ENST00000368174 NM_005894.3 +LYSMD1 ENST00000368908 NM_212551.5 +CD2 ENST00000369478 NM_001767.5 +DEPDC1 ENST00000456315 NM_001114120.3 +GPR89A ENST00000313835 NM_001097612.2 +GTF2B ENST00000370500 NM_001514.6 +TNFSF4 ENST00000281834 NM_003326.5 +KCNJ9 ENST00000368088 NM_004983.3 +CSF1 ENST00000329608 NM_000757.6 +TNFAIP8L2 ENST00000368910 NM_024575.5 +IGSF8 ENST00000314485 NM_052868.6 +MPC2 ENST00000271373 NM_001143674.4 +FIRRM ENST00000359326 NM_001320047.2 +LAMC1 ENST00000258341 NM_002293.4 +MGST3 ENST00000367889 NM_004528.4 +CASQ1 ENST00000368078 NM_001231.5 +ILF2 ENST00000361891 NM_004515.4 +NME7 ENST00000367811 NM_013330.5 +RCSD1 ENST00000367854 NM_052862.4 +SFT2D2 ENST00000271375 NM_199344.3 +UCK2 ENST00000367879 NM_012474.5 +PIGM ENST00000368090 NM_145167.3 +XCL2 ENST00000367819 NM_003175.4 +POU2F1 ENST00000367866 NM_002697.4 +KIFAP3 ENST00000361580 NM_014970.4 +TBX15 ENST00000369429 NM_001330677.2 +CD48 ENST00000368046 NM_001778.4 +RXRG ENST00000359842 NM_006917.5 +TPR ENST00000367478 NM_003292.3 +ATP1A2 ENST00000361216 NM_000702.4 +METTL18 ENST00000310392 NM_033418.4 +CHIA ENST00000369740 NM_201653.4 +EXTL2 ENST00000370114 NM_001033025.3 +DDX59 ENST00000331314 NM_001031725.6 +NIBAN1 ENST00000367511 NM_052966.4 +OR10J5 ENST00000334857 NM_001004469.1 +LAMC2 ENST00000264144 NM_005562.3 +CD58 ENST00000369489 NM_001779.3 +GPA33 ENST00000367868 NM_005814.3 +XCL1 ENST00000367818 NM_002995.3 +KCNJ10 ENST00000644903 NM_002241.5 +NUF2 ENST00000271452 NM_145697.3 +MFSD4A ENST00000367147 NM_181644.5 +TBX19 ENST00000367821 NM_005149.3 +NR5A2 ENST00000367362 NM_205860.3 +SCYL3 ENST00000367771 NM_020423.7 +DUSP10 ENST00000366899 NM_007207.6 +NMNAT2 ENST00000287713 NM_015039.4 +TARBP1 ENST00000040877 NM_005646.4 +LY9 ENST00000263285 NM_002348.4 +TDRD5 ENST00000444136 NM_001199085.3 +SCCPDH ENST00000366510 NM_016002.3 +ELK4 ENST00000357992 NM_001973.4 +TFB2M ENST00000366514 NM_022366.3 +LYPLAL1 ENST00000366928 NM_138794.5 +MPZL1 ENST00000359523 NM_003953.6 +INTS7 ENST00000366994 NM_015434.4 +CATSPERE ENST00000366534 NM_001130957.2 +PRDX6 ENST00000340385 NM_004905.3 +EDARADD ENST00000334232 NM_145861.4 +BRINP3 ENST00000367462 NM_199051.3 +LMX1A ENST00000342310 NM_177398.4 +ADCY10 ENST00000367851 NM_018417.6 +SELE ENST00000333360 NM_000450.2 +GPATCH2 ENST00000366935 NM_018040.5 +SMYD2 ENST00000366957 NM_020197.3 +SELL ENST00000236147 NM_000655.5 +DPT ENST00000367817 NM_001937.5 +CAPN8 ENST00000366872 NM_001143962.2 +RHOU ENST00000366691 NM_021205.6 +RNF2 ENST00000367510 NM_007212.4 +RGS5 ENST00000313961 NM_003617.4 +SPATA17 ENST00000366933 NM_138796.4 +PRRX1 ENST00000239461 NM_022716.4 +IVNS1ABP ENST00000367498 NM_006469.5 +ASTN1 ENST00000361833 NM_004319.3 +DTL ENST00000366991 NM_016448.4 +TRMT1L ENST00000367506 NM_030934.5 +SOAT1 ENST00000367619 NM_003101.6 +CNST ENST00000366513 NM_152609.3 +SOX13 ENST00000367204 NM_005686.3 +NID1 ENST00000264187 NM_002508.3 +ZNF678 ENST00000343776 NM_001367909.1 +SLC9C2 ENST00000367714 NM_178527.4 +LHX9 ENST00000367387 NM_020204.3 +DESI2 ENST00000302550 NM_016076.5 +SLC26A9 ENST00000367135 NM_052934.4 +SLC45A3 ENST00000367145 NM_033102.3 +ILDR2 ENST00000271417 NM_199351.3 +KIF26B ENST00000407071 NM_018012.4 +RRP15 ENST00000366932 NM_016052.4 +PTPN14 ENST00000366956 NM_005401.5 +NEK2 ENST00000366999 NM_002497.4 +C1orf53 ENST00000367393 NM_001024594.3 +RAB4A ENST00000366690 NM_004578.4 +TOMM20 ENST00000366607 NM_014765.3 +TADA1 ENST00000367874 NM_053053.4 +REN ENST00000272190 NM_000537.4 +DHX9 ENST00000367549 NM_001357.5 +BTF3L4 ENST00000313334 NM_152265.5 +SWT1 ENST00000367500 NM_017673.7 +COP1 ENST00000367669 NM_022457.7 +SLAMF7 ENST00000368043 NM_021181.5 +RGS18 ENST00000367460 NM_130782.3 +GNPAT ENST00000366647 NM_014236.4 +TGFB2 ENST00000366930 NM_003238.6 +ODR4 ENST00000287859 NM_017847.6 +FMO4 ENST00000367749 NM_002022.3 +NSL1 ENST00000366977 NM_015471.4 +HFM1 ENST00000370425 NM_001017975.6 +ATP1A4 ENST00000368081 NM_144699.4 +GALNT2 ENST00000366672 NM_004481.5 +FMO1 ENST00000617670 NM_001282693.2 +SPRTN ENST00000295050 NM_032018.7 +EGLN1 ENST00000366641 NM_022051.3 +FCRL1 ENST00000368176 NM_052938.5 +GNG4 ENST00000391854 NM_001098722.2 +PAPPA2 ENST00000367662 NM_020318.3 +LRRN2 ENST00000367177 NM_201630.2 +PPP2R5A ENST00000261461 NM_006243.4 +SPMIP3 ENST00000308105 NM_001012970.3 +RNASEL ENST00000367559 NM_021133.4 +SPATA45 ENST00000332912 NM_001024601.3 +PLA2G4A ENST00000367466 NM_024420.3 +ETNK2 ENST00000367202 NM_018208.4 +SHCBP1L ENST00000367547 NM_030933.4 +LPGAT1 ENST00000366997 NM_014873.3 +PFKFB2 ENST00000367080 NM_006212.2 +TATDN3 ENST00000366974 NM_001042552.3 +SELP ENST00000263686 NM_003005.4 +CAMK1G ENST00000361322 NM_020439.3 +ZNF672 ENST00000306562 NM_024836.3 +LAMB3 ENST00000356082 NM_000228.3 +ARHGEF10L ENST00000361221 NM_018125.4 +NOS1AP ENST00000361897 NM_014697.3 +ANGEL2 ENST00000366962 NM_144567.5 +RGSL1 ENST00000294854 NM_001137669.2 +EXOC8 ENST00000366645 NM_175876.5 +BRINP2 ENST00000361539 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NM_173853.4 +FNDC4 ENST00000264703 NM_022823.3 +IFT172 ENST00000260570 NM_015662.3 +NIFK ENST00000285814 NM_032390.5 +TSN ENST00000389682 NM_004622.3 +ACVR2A ENST00000241416 NM_001616.5 +ORC4 ENST00000392857 NM_181741.4 +MBD5 ENST00000642680 NM_001378120.1 +RGPD5 ENST00000016946 NM_005054.3 +MALL ENST00000272462 NM_005434.5 +NPHP1 ENST00000445609 NM_001128178.3 +LCLAT1 ENST00000379509 NM_001002257.3 +NOSTRIN ENST00000317647 NM_001039724.4 +WDSUB1 ENST00000359774 NM_001128212.3 +EHBP1 ENST00000431489 NM_001142616.3 +VRK2 ENST00000340157 NM_006296.7 +STON1 ENST00000404752 NM_006873.4 +ERMN ENST00000410096 NM_020711.3 +CERS6 ENST00000305747 NM_203463.3 +UBE2F ENST00000272930 NM_080678.3 +DYNC1I2 ENST00000397119 NM_001378.3 +MTA3 ENST00000405094 NM_001330442.2 +IDH1 ENST00000345146 NM_005896.4 +EIPR1 ENST00000382125 NM_003310.5 +MYO3B ENST00000408978 NM_138995.5 +TIGD1 ENST00000408957 NM_145702.4 +CFAP36 ENST00000349456 NM_080667.7 +CCDC150 ENST00000389175 NM_001080539.2 +GTF3C3 ENST00000263956 NM_012086.5 +C2orf66 ENST00000342506 NM_213608.3 +PGAP1 ENST00000354764 NM_024989.4 +IL1R1 ENST00000410023 NM_000877.4 +IL1RL2 ENST00000264257 NM_003854.4 +IL1RL1 ENST00000233954 NM_016232.5 +SLC9A4 ENST00000295269 NM_001011552.4 +LIPT1 ENST00000651691 NM_145199.3 +MITD1 ENST00000289359 NM_138798.3 +MRPL30 ENST00000338148 NM_145212.4 +LYG1 ENST00000308528 NM_174898.3 +TXNDC9 ENST00000264255 NM_005783.4 +C2orf69 ENST00000319974 NM_153689.6 +TYW5 ENST00000354611 NM_001039693.3 +TFCP2L1 ENST00000263707 NM_014553.3 +TRIM43 ENST00000272395 NM_138800.3 +SF3B1 ENST00000335508 NM_012433.4 +HSPE1 ENST00000233893 NM_002157.3 +MOB4 ENST00000323303 NM_015387.5 +CFAP210 ENST00000447353 NM_001085447.2 +PHOSPHO2 ENST00000359744 NM_001008489.4 +KLHL23 ENST00000392647 NM_144711.6 +SSB ENST00000260956 NM_003142.5 +METTL5 ENST00000260953 NM_014168.4 +HSPD1 ENST00000388968 NM_002156.5 +UBR3 ENST00000272793 NM_172070.4 +GCG ENST00000418842 NM_002054.5 +IFT70B ENST00000408939 NM_152517.3 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ENST00000282701 NM_001201.5 +PRKG2 ENST00000264399 NM_006259.3 +BMPR1B ENST00000515059 NM_001203.3 +UNC5C ENST00000453304 NM_003728.4 +EIF4E ENST00000450253 NM_001968.5 +METAP1 ENST00000296411 NM_015143.3 +ADH5 ENST00000296412 NM_000671.4 +ADH4 ENST00000265512 NM_000670.5 +ADH6 ENST00000394899 NM_001102470.2 +ADH1A ENST00000209668 NM_000667.4 +ADH1B ENST00000305046 NM_000668.6 +ADH1C ENST00000515683 NM_000669.5 +PACRGL ENST00000503585 NM_001258345.3 +KCNIP4 ENST00000382152 NM_025221.6 +ARL9 ENST00000640821 NM_001363794.2 +HOPX ENST00000420433 NM_032495.6 +DUX4 ENST00000565211 NM_001306068.3 +TMEM129 ENST00000382936 NM_001127266.2 +CHRNA9 ENST00000310169 NM_017581.4 +RBM47 ENST00000295971 NM_001098634.2 +APBB2 ENST00000508593 NM_004307.2 +TMEM33 ENST00000504986 NM_018126.3 +ADAMTS3 ENST00000286657 NM_014243.3 +AFP ENST00000395792 NM_001134.3 +AFM ENST00000226355 NM_001133.2 +PPEF2 ENST00000286719 NM_006239.3 +RPS3A ENST00000274065 NM_001006.5 +SH3D19 ENST00000604030 NM_001378122.1 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NM_004934.5 +RAI14 ENST00000265109 NM_015577.3 +CDH12 ENST00000382254 NM_004061.5 +FGF10 ENST00000264664 NM_004465.2 +RAB3C ENST00000282878 NM_138453.4 +C5orf34 ENST00000306862 NM_198566.4 +EMB ENST00000303221 NM_198449.3 +ELOVL7 ENST00000508821 NM_024930.3 +ITGA1 ENST00000282588 NM_181501.2 +FAM151B ENST00000282226 NM_205548.3 +CCDC152 ENST00000361970 NM_001134848.2 +MTREX ENST00000230640 NM_015360.5 +TMEM167A ENST00000502346 NM_174909.5 +HAPLN1 ENST00000274341 NM_001884.4 +VCAN ENST00000265077 NM_004385.5 +OXCT1 ENST00000196371 NM_000436.4 +SUB1 ENST00000265073 NM_006713.4 +CAPSL ENST00000651391 NM_001042625.2 +TRAPPC13 ENST00000399438 NM_024941.4 +GZMK ENST00000231009 NM_002104.3 +ARSB ENST00000264914 NM_000046.5 +CENPK ENST00000396679 NM_022145.5 +PDZD2 ENST00000438447 NM_178140.4 +ZSWIM6 ENST00000252744 NM_020928.2 +ITGA2 ENST00000296585 NM_002203.4 +JMY ENST00000396137 NM_152405.5 +GDNF ENST00000326524 NM_000514.4 +SERINC5 ENST00000507668 NM_001174072.3 +NIPBL ENST00000282516 NM_133433.4 +CKMT2 ENST00000254035 NM_001099735.2 +SHLD3 ENST00000510585 NM_001365341.2 +ATG10 ENST00000282185 NM_031482.5 +RASGRF2 ENST00000265080 NM_006909.3 +SGTB ENST00000381007 NM_019072.3 +GOLPH3 ENST00000265070 NM_022130.4 +ANKRD34B ENST00000338682 NM_001004441.3 +ACTBL2 ENST00000423391 NM_001017992.4 +NUDT12 ENST00000230792 NM_031438.4 +GPBP1 ENST00000506184 NM_022913.4 +MSH3 ENST00000265081 NM_002439.5 +SPZ1 ENST00000296739 NM_032567.4 +CD180 ENST00000256447 NM_005582.3 +IL7R ENST00000303115 NM_002185.5 +COX7C ENST00000247655 NM_001867.3 +RGS7BP ENST00000334025 NM_001029875.3 +CCNO ENST00000282572 NM_021147.5 +PRLR ENST00000618457 NM_000949.7 +CAMK4 ENST00000282356 NM_001744.6 +NDUFS4 ENST00000296684 NM_002495.4 +STARD4 ENST00000296632 NM_139164.3 +PCSK1 ENST00000311106 NM_000439.5 +FAM172A ENST00000395965 NM_032042.6 +DMGDH ENST00000255189 NM_013391.3 +CMYA5 ENST00000446378 NM_153610.5 +PLPP1 ENST00000307259 NM_003711.4 +ATG12 ENST00000509910 NM_004707.4 +SPMIP10 ENST00000357147 NM_207408.3 +ADGRV1 ENST00000405460 NM_032119.4 +PJA2 ENST00000361189 NM_014819.5 +FCHO2 ENST00000430046 NM_138782.3 +MEGF10 ENST00000503335 NM_001256545.2 +CSF2 ENST00000296871 NM_000758.4 +GRAMD2B ENST00000285689 NM_023927.4 +TRIM23 ENST00000231524 NM_001656.4 +HCN1 ENST00000303230 NM_021072.4 +CDO1 ENST00000250535 NM_001801.3 +EGFLAM ENST00000322350 NM_152403.4 +DTWD2 ENST00000510708 NM_173666.4 +EPB41L4A ENST00000261486 NM_022140.5 +RAD50 ENST00000378823 NM_005732.4 +AP3S1 ENST00000316788 NM_001284.4 +ARRDC3 ENST00000265138 NM_020801.4 +SLC25A46 ENST00000355943 NM_138773.4 +LMNB1 ENST00000261366 NM_005573.4 +NREP ENST00000257435 NM_004772.4 +IL9 ENST00000274520 NM_000590.2 +BHMT2 ENST00000255192 NM_017614.5 +EDIL3 ENST00000296591 NM_005711.5 +PHAX ENST00000297540 NM_032177.4 +NIM1K ENST00000326035 NM_153361.4 +RIOK2 ENST00000283109 NM_018343.3 +IRX1 ENST00000302006 NM_024337.4 +PRR16 ENST00000407149 NM_001300783.2 +LECT2 ENST00000274507 NM_002302.3 +CDH6 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ENST00000297109 NM_024632.6 +NRG2 ENST00000361474 NM_004883.3 +FAM200C ENST00000408953 NM_022090.5 +KIF20A ENST00000394894 NM_005733.3 +FAM174A ENST00000312637 NM_198507.3 +COMMD10 ENST00000274458 NM_016144.4 +TNFAIP8 ENST00000504771 NM_014350.4 +DHFR ENST00000439211 NM_000791.4 +SH3PXD2B ENST00000311601 NM_001017995.3 +KCTD16 ENST00000512467 NM_020768.4 +HAND1 ENST00000231121 NM_004821.3 +PTTG1 ENST00000352433 NM_004219.4 +IL3 ENST00000296870 NM_000588.4 +ARHGAP26 ENST00000645722 NM_001135608.3 +SCGB3A2 ENST00000296694 NM_054023.5 +DELE1 ENST00000432126 NM_014773.5 +GABRA1 ENST00000393943 NM_001127644.2 +ELL2 ENST00000237853 NM_012081.6 +GFPT2 ENST00000253778 NM_005110.4 +FGF1 ENST00000337706 NM_000800.5 +MSX2 ENST00000239243 NM_002449.5 +BOD1 ENST00000311086 NM_138369.3 +SLU7 ENST00000297151 NM_006425.5 +ARAP3 ENST00000239440 NM_022481.6 +ATP10B ENST00000327245 NM_025153.3 +RANBP17 ENST00000523189 NM_022897.5 +FTMT ENST00000321339 NM_177478.2 +NSG2 ENST00000303177 NM_015980.5 +NR3C1 ENST00000394464 NM_000176.3 +BTNL8 ENST00000340184 NM_001040462.3 +LIFR ENST00000453190 NM_001127671.2 +RASA1 ENST00000274376 NM_002890.3 +MRPL22 ENST00000523037 NM_014180.4 +TMEM232 ENST00000455884 NM_001039763.4 +ALDH7A1 ENST00000409134 NM_001182.5 +C5orf47 ENST00000340147 NM_001144954.2 +NKX2-5 ENST00000329198 NM_004387.4 +ADRA1B ENST00000306675 NM_000679.4 +PTGER4 ENST00000302472 NM_000958.3 +ARHGEF37 ENST00000333677 NM_001001669.3 +NLN ENST00000380985 NM_020726.5 +DRD1 ENST00000393752 NM_000794.5 +SYNPO ENST00000307662 NM_007286.6 +SIL1 ENST00000394817 NM_022464.5 +CNOT6 ENST00000261951 NM_001370472.1 +RNF14 ENST00000394520 NM_004290.5 +NEURL1B ENST00000369800 NM_001142651.3 +ZFYVE16 ENST00000505560 NM_001284236.3 +BTNL3 ENST00000342868 NM_197975.3 +SOX30 ENST00000265007 NM_178424.2 +SFXN1 ENST00000321442 NM_022754.7 +C5orf52 ENST00000409999 NM_001145132.2 +KIF4B ENST00000435029 NM_001099293.3 +CHSY3 ENST00000305031 NM_175856.5 +C5orf46 ENST00000318315 NM_206966.3 +SOWAHA 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ENST00000683689 NM_001384609.1 +ATP11A ENST00000375645 NM_015205.3 +CYSLTR2 ENST00000682523 NM_001308476.3 +OXGR1 ENST00000541038 NM_001346194.2 +COMMD6 ENST00000682242 NM_203495.4 +THSD1 ENST00000258613 NM_018676.4 +VPS36 ENST00000378060 NM_016075.4 +CKAP2 ENST00000258607 NM_018204.5 +SUGT1 ENST00000310528 NM_006704.5 +HNRNPA1L2 ENST00000357495 NM_001389320.1 +DAOA ENST00000375936 NM_172370.5 +ZIC2 ENST00000376335 NM_007129.5 +ZIC5 ENST00000267294 NM_033132.5 +LNX2 ENST00000316334 NM_153371.4 +GSX1 ENST00000302945 NM_145657.3 +PDX1 ENST00000381033 NM_000209.4 +POLR1D ENST00000302979 NM_015972.4 +LIG4 ENST00000442234 NM_206937.2 +CLYBL ENST00000339105 NM_206808.5 +ITGBL1 ENST00000376180 NM_004791.3 +SUPT20H ENST00000350612 NM_001014286.3 +C13orf42 ENST00000563710 NM_001351589.3 +NBEA ENST00000379939 NM_001385012.1 +SETDB2 ENST00000611815 NM_001160308.3 +PHF11 ENST00000378319 NM_001040443.3 +RCBTB1 ENST00000378302 NM_018191.4 +SKA3 ENST00000314759 NM_145061.6 +MRPL57 ENST00000309594 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NM_003701.4 +TPP2 ENST00000376052 NM_001330588.2 +ALG11 ENST00000521508 NM_001004127.3 +NUP58 ENST00000381736 NM_014089.4 +N4BP2L2 ENST00000267068 NM_014887.3 +C1QTNF9 ENST00000332018 NM_178540.5 +LRRC63 ENST00000595396 NM_001282460.2 +ENSG00000285566 ENST00000648713 NM_001370368.2 +PCDH20 ENST00000409204 NM_022843.4 +SAP18 ENST00000382533 NM_005870.5 +ATP12A ENST00000381946 NM_001676.7 +RNF17 ENST00000255324 NM_031277.3 +ARHGEF7 ENST00000646102 NM_001354046.2 +CDK8 ENST00000381527 NM_001260.3 +CFAP97D2 ENST00000636692 NM_001395229.1 +CDC16 ENST00000356221 NM_001078645.3 +UPF3A ENST00000375299 NM_023011.4 +CHAMP1 ENST00000361283 NM_032436.4 +NDFIP2 ENST00000218652 NM_019080.3 +DOCK9 ENST00000682017 NM_001366683.2 +HSPH1 ENST00000320027 NM_006644.4 +B3GLCT ENST00000343307 NM_194318.4 +ZDHHC20 ENST00000400590 NM_001330059.2 +MBNL2 ENST00000679496 NM_001382683.1 +F7 ENST00000346342 NM_019616.4 +F10 ENST00000375559 NM_000504.4 +PROZ ENST00000375547 NM_003891.3 +PCID2 ENST00000337344 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+FOXA2 ENST00000419308 NM_021784.5 +POLR3F ENST00000377603 NM_006466.4 +RBBP9 ENST00000337227 NM_006606.3 +SEC23B ENST00000650089 NM_006363.6 +SMIM26 ENST00000411646 NM_001348957.2 +RBCK1 ENST00000356286 NM_031229.4 +SPO11 ENST00000371263 NM_012444.3 +RAE1 ENST00000395841 NM_003610.4 +RBM38 ENST00000356208 NM_017495.6 +ACOT8 ENST00000217455 NM_005469.4 +DEFB121 ENST00000376314 NM_001011878.3 +DEFB123 ENST00000376309 NM_153324.4 +DEFB124 ENST00000317676 NM_001037500.2 +REM1 ENST00000201979 NM_014012.6 +TM9SF4 ENST00000398022 NM_014742.4 +KIF3B ENST00000375712 NM_004798.4 +NOL4L ENST00000621426 NM_001256798.2 +SULF2 ENST00000688720 NM_001387048.1 +HELZ2 ENST00000467148 NM_001037335.2 +YWHAB ENST00000353703 NM_139323.4 +PABPC1L ENST00000217073 NM_001372179.1 +TOMM34 ENST00000372813 NM_006809.5 +KCNS1 ENST00000537075 NM_001322799.2 +WFDC12 ENST00000372785 NM_080869.2 +PI3 ENST00000243924 NM_002638.4 +SEMG1 ENST00000372781 NM_003007.5 +SEMG2 ENST00000372769 NM_003008.3 +STK4 ENST00000372806 NM_006282.5 +DEFB116 ENST00000400549 NM_001037731.1 +DEFB118 ENST00000253381 NM_054112.3 +DEFB119 ENST00000376321 NM_153289.4 +PAX1 ENST00000613128 NM_001257096.2 +ZNF341 ENST00000375200 NM_001282933.2 +ZNF133 ENST00000425686 NM_001352452.2 +CHGB ENST00000378961 NM_001819.3 +TRMT6 ENST00000203001 NM_015939.5 +MCM8 ENST00000610722 NM_032485.6 +CRLS1 ENST00000378863 NM_019095.6 +LRRN4 ENST00000378858 NM_152611.5 +ATRN ENST00000262919 NM_139321.3 +GFRA4 ENST00000290417 NM_022139.4 +SMOX ENST00000305958 NM_175839.3 +FERMT1 ENST00000217289 NM_017671.5 +DZANK1 ENST00000699568 NM_001367614.1 +MCTS2 ENST00000394552 NM_001397496.1 +ADNP ENST00000621696 NM_001282531.3 +WFDC5 ENST00000372789 NM_145652.4 +EBF4 ENST00000609451 NM_001395167.1 +TTLL9 ENST00000535842 NM_001008409.5 +MYT1 ENST00000328439 NM_004535.3 +NPBWR2 ENST00000684052 NM_005286.4 +PCMTD2 ENST00000308824 NM_018257.3 +SSTR4 ENST00000255008 NM_001052.4 +THBD ENST00000377103 NM_000361.3 +CD93 ENST00000246006 NM_012072.4 +RGS19 ENST00000395042 NM_005873.3 +LKAAEAR1 ENST00000302096 NM_001353425.2 +EMILIN3 ENST00000332312 NM_052846.2 +GPCPD1 ENST00000379019 NM_019593.5 +LIME1 ENST00000309546 NM_017806.4 +ABHD16B ENST00000369916 NM_080622.4 +TPD52L2 ENST00000346249 NM_003288.4 +DNAJC5 ENST00000360864 NM_025219.3 +UCKL1 ENST00000354216 NM_017859.4 +ZNF512B ENST00000369888 NM_020713.3 +SAMD10 ENST00000369886 NM_080621.5 +SEL1L2 ENST00000284951 NM_025229.2 +MACROD2 ENST00000684519 NM_001351661.2 +FLRT3 ENST00000341420 NM_198391.3 +L3MBTL1 ENST00000418998 NM_001377303.1 +RPN2 ENST00000237530 NM_002951.5 +WFDC6 ENST00000372670 NM_080827.2 +SNAP25 ENST00000254976 NM_130811.4 +POFUT1 ENST00000375749 NM_015352.2 +NANP ENST00000304788 NM_152667.3 +ZNF337 ENST00000252979 NM_015655.4 +CEP250 ENST00000397527 NM_007186.6 +HNF4A ENST00000316673 NM_175914.5 +CTSA ENST00000646241 NM_000308.4 +EEF1A2 ENST00000217182 NM_001958.5 +KCNQ2 ENST00000359125 NM_172107.4 +BLCAP ENST00000373537 NM_006698.4 +NNAT ENST00000649451 NM_005386.4 +NINL ENST00000278886 NM_025176.6 +OPRL1 ENST00000336866 NM_182647.4 +SIGLEC1 ENST00000344754 NM_023068.4 +EDEM2 ENST00000374492 NM_018217.3 +UQCC1 ENST00000374385 NM_018244.5 +HAO1 ENST00000378789 NM_017545.3 +TMX4 ENST00000246024 NM_021156.4 +PLCB1 ENST00000338037 NM_015192.4 +TSHZ2 ENST00000371497 NM_173485.6 +ZNF217 ENST00000371471 NM_006526.3 +KIF16B ENST00000354981 NM_024704.5 +TP53INP2 ENST00000374810 NM_021202.3 +GGT7 ENST00000336431 NM_178026.3 +ACSS2 ENST00000360596 NM_018677.4 +MYH7B ENST00000262873 NM_020884.7 +PTPRT ENST00000373187 NM_007050.6 +HM13 ENST00000398174 NM_178581.3 +GNAS ENST00000371075 NM_016592.5 +GNAS ENST00000371100 NM_080425.4 +GNAS ENST00000371085 NM_000516.7 +RTEL1 ENST00000360203 NM_001283009.2 +ASXL1 ENST00000375687 NM_015338.6 +BPIFA1 ENST00000354297 NM_130852.3 +VSTM2L ENST00000373461 NM_080607.3 +TTI1 ENST00000373447 NM_001303457.2 +RPRD1B ENST00000373433 NM_021215.4 +TGM2 ENST00000361475 NM_004613.4 +KIAA1755 ENST00000279024 NM_001029864.2 +RAB22A ENST00000244040 NM_020673.3 +VAPB ENST00000475243 NM_004738.5 +APCDD1L ENST00000371149 NM_153360.3 +STX16 ENST00000371141 NM_001001433.3 +PANK2 ENST00000610179 NM_001386393.1 +ENSG00000285508 ENST00000713549 NM_001394149.2 +ENSG00000285723 ENST00000649912 NM_001394148.2 +CTNNBL1 ENST00000361383 NM_030877.5 +TMPRSS15 ENST00000284885 NM_002772.3 +CXADR ENST00000284878 NM_001338.5 +URB1 ENST00000382751 NM_014825.3 +KRTAP25-1 ENST00000416044 NM_001128598.1 +JAM2 ENST00000480456 NM_021219.4 +CLDN17 ENST00000286808 NM_012131.3 +CYYR1 ENST00000652641 NM_001320768.2 +MRPS6 ENST00000399312 NM_032476.4 +KRTAP24-1 ENST00000340345 NM_001085455.3 +SLC5A3 ENST00000381151 NM_006933.7 +CHAF1B ENST00000314103 NM_005441.3 +SCAF4 ENST00000286835 NM_020706.2 +NCAM2 ENST00000400546 NM_004540.5 +CLDN8 ENST00000399899 NM_199328.3 +C21orf140 ENST00000410005 NM_001282537.2 +HUNK ENST00000270112 NM_014586.2 +C21orf91 ENST00000284881 NM_001100420.2 +MORC3 ENST00000400485 NM_015358.3 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NM_005069.6 +RIPPLY3 ENST00000329553 NM_018962.3 +RRP1B ENST00000340648 NM_015056.3 +PDXK ENST00000291565 NM_003681.5 +RRP1 ENST00000497547 NM_003683.6 +AGPAT3 ENST00000291572 NM_020132.5 +TRAPPC10 ENST00000291574 NM_003274.5 +PWP2 ENST00000291576 NM_005049.3 +DYRK1A ENST00000647188 NM_001347721.2 +PRDM15 ENST00000398548 NM_001040424.3 +PKNOX1 ENST00000291547 NM_004571.5 +CBS ENST00000398165 NM_000071.3 +CRYAA ENST00000291554 NM_000394.4 +U2AF1 ENST00000291552 NM_006758.3 +SETD4 ENST00000332131 NM_017438.5 +SLC19A1 ENST00000311124 NM_194255.4 +COL18A1 ENST00000651438 NM_001379500.1 +FAM3B ENST00000357985 NM_058186.4 +ADAMTS1 ENST00000284984 NM_006988.5 +MIS18A ENST00000290130 NM_018944.3 +MRAP ENST00000303645 NM_001379228.1 +WDR4 ENST00000398208 NM_018669.6 +NDUFV3 ENST00000354250 NM_021075.4 +GABPA ENST00000400075 NM_002040.4 +CLIC6 ENST00000349499 NM_053277.3 +PIGP ENST00000360525 NM_153682.3 +KCNE2 ENST00000290310 NM_172201.2 +TPTE ENST00000618007 NM_199261.4 +SYNJ1 ENST00000674351 NM_203446.3 +RBM11 ENST00000400577 NM_144770.5 +HSPA13 ENST00000285667 NM_006948.5 +PSMG1 ENST00000331573 NM_003720.4 +BRWD1 ENST00000342449 NM_033656.4 +HMGN1 ENST00000380749 NM_004965.7 +GET1 ENST00000649170 NM_004627.6 +PCP4 ENST00000328619 NM_006198.3 +DSCAM ENST00000400454 NM_001389.5 +BACE2 ENST00000330333 NM_012105.5 +RIPK4 ENST00000332512 NM_020639.3 +ABCG1 ENST00000398449 NM_016818.3 +TFF2 ENST00000291526 NM_005423.5 +TFF1 ENST00000291527 NM_003225.3 +TMPRSS3 ENST00000644384 NM_001256317.3 +UBASH3A ENST00000319294 NM_018961.4 +RSPH1 ENST00000291536 NM_080860.4 +SLC37A1 ENST00000352133 NM_001320537.2 +PDE9A ENST00000291539 NM_002606.3 +SIK1 ENST00000270162 NM_173354.5 +HSF2BP ENST00000291560 NM_007031.2 +H2BC12L ENST00000599962 NM_017445.3 +DNMT3L ENST00000628202 NM_175867.3 +AIRE ENST00000291582 NM_000383.4 +PFKL ENST00000349048 NM_002626.6 +CFAP410 ENST00000339818 NM_004928.3 +LRRC3 ENST00000291592 NM_030891.6 +TSPEAR ENST00000323084 NM_144991.3 +KRTAP10-1 ENST00000400375 NM_198691.3 +KRTAP10-2 ENST00000391621 NM_198693.4 +KRTAP10-3 ENST00000391620 NM_198696.3 +KRTAP10-5 ENST00000400372 NM_198694.3 +KRTAP10-6 ENST00000400368 NM_198688.3 +KRTAP10-7 ENST00000609664 NM_198689.3 +KRTAP10-8 ENST00000334662 NM_198695.2 +KRTAP10-10 ENST00000380095 NM_181688.3 +KRTAP10-11 ENST00000334670 NM_198692.3 +KRTAP12-4 ENST00000391618 NM_198698.1 +KRTAP12-3 ENST00000397907 NM_198697.2 +KRTAP12-2 ENST00000360770 NM_181684.3 +KRTAP12-1 ENST00000391617 NM_181686.2 +UBE2G2 ENST00000345496 NM_003343.6 +PTTG1IP ENST00000330938 NM_004339.4 +POFUT2 ENST00000349485 NM_133635.6 +PCBP3 ENST00000681687 NM_001384156.1 +TMPRSS2 ENST00000332149 NM_005656.4 +MX1 ENST00000398598 NM_002462.5 +MX2 ENST00000330714 NM_002463.2 +LCA5L ENST00000288350 NM_152505.4 +ATP5PF ENST00000284971 NM_001003703.2 +SPATC1L ENST00000291672 NM_001142854.2 +LSS ENST00000397728 NM_002340.6 +FTCD ENST00000397746 NM_206965.2 +HLCS ENST00000674895 NM_001352514.2 +KCNE1 ENST00000399286 NM_000219.6 +COL6A1 ENST00000361866 NM_001848.3 +OLIG2 ENST00000382357 NM_005806.4 +OLIG1 ENST00000382348 NM_138983.3 +TFF3 ENST00000518498 NM_003226.4 +POTED ENST00000299443 NM_174981.6 +UMODL1 ENST00000408910 NM_001004416.3 +USP25 ENST00000400183 NM_001283041.3 +KRTAP8-1 ENST00000329621 NM_175857.4 +KRTAP7-1 ENST00000621162 NM_181606.3 +KRTAP11-1 ENST00000332378 NM_175858.3 +KRTAP19-8 ENST00000382822 NM_001099219.1 +SOD1 ENST00000270142 NM_000454.5 +DOP1B ENST00000691173 NM_001320714.2 +ERVH48-1 ENST00000447535 NM_001308491.2 +LIPI ENST00000681601 NM_001302998.2 +KRTAP10-9 ENST00000397911 NM_198690.3 +PRMT2 ENST00000355680 NM_206962.4 +ERG ENST00000288319 NM_182918.4 +KRTAP10-4 ENST00000400374 NM_198687.2 +TRPM2 ENST00000397928 NM_003307.4 +IGSF5 ENST00000380588 NM_001080444.2 +B3GALT5 ENST00000684187 NM_001356336.2 +MCM3AP ENST00000291688 NM_003906.5 +YBEY ENST00000397701 NM_001314025.2 +C21orf58 ENST00000291691 NM_058180.5 +DIP2A ENST00000417564 NM_015151.4 +GART ENST00000381815 NM_000819.5 +DONSON ENST00000303071 NM_017613.4 +TMEM50B ENST00000542230 NM_006134.7 +IL10RB ENST00000290200 NM_000628.5 +IFNGR2 ENST00000290219 NM_005534.4 +VPS26C ENST00000309117 NM_006052.2 +TTC3 ENST00000418766 NM_001330683.2 +ITGB2 ENST00000652462 NM_000211.5 +KRTAP26-1 ENST00000360542 NM_203405.2 +KRTAP27-1 ENST00000382835 NM_001077711.1 +KRTAP13-2 ENST00000399889 NM_181621.4 +KRTAP13-1 ENST00000355459 NM_181599.3 +KRTAP15-1 ENST00000334067 NM_181623.3 +KRTAP19-1 ENST00000390689 NM_181607.3 +KRTAP19-2 ENST00000334055 NM_181608.2 +KRTAP19-3 ENST00000334063 NM_181609.4 +KRTAP19-4 ENST00000334058 NM_181610.3 +KRTAP19-5 ENST00000334151 NM_181611.3 +KRTAP19-6 ENST00000334046 NM_181612.3 +KRTAP19-7 ENST00000334849 NM_181614.3 +KRTAP22-2 ENST00000382830 NM_001164434.1 +KRTAP6-3 ENST00000391624 NM_181605.4 +KRTAP22-1 ENST00000334680 NM_181620.2 +KRTAP20-1 ENST00000334664 NM_181615.2 +KRTAP20-4 ENST00000382828 NM_001350977.1 +KRTAP20-2 ENST00000330798 NM_181616.3 +KRTAP20-3 ENST00000382826 NM_001128077.1 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+COL6A2 ENST00000397763 NM_058174.3 +COL6A2 ENST00000300527 NM_001849.4 +DNAJC28 ENST00000381947 NM_001040192.3 +SLX9 ENST00000291634 NM_058190.4 +KCNJ6 ENST00000609713 NM_002240.5 +CSTB ENST00000291568 NM_000100.4 +ENSG00000286224 ENST00000652508 NM_001414902.1 +CCT8L2 ENST00000359963 NM_014406.5 +MED15 ENST00000263205 NM_001003891.3 +OSM ENST00000215781 NM_020530.6 +DRG1 ENST00000331457 NM_004147.4 +HORMAD2 ENST00000336726 NM_152510.4 +NCF4 ENST00000248899 NM_000631.5 +SFI1 ENST00000400288 NM_001007467.3 +CACNA1I ENST00000402142 NM_021096.4 +TNRC6B ENST00000454349 NM_001162501.2 +ISX ENST00000404699 NM_001303508.2 +MCAT ENST00000290429 NM_173467.5 +ENTHD1 ENST00000325157 NM_152512.4 +LIF ENST00000249075 NM_002309.5 +CBX7 ENST00000216133 NM_175709.5 +PNPLA3 ENST00000216180 NM_025225.3 +EFCAB6 ENST00000262726 NM_022785.4 +TBC1D22A ENST00000337137 NM_014346.5 +ZBED4 ENST00000216268 NM_014838.3 +RPL3 ENST00000216146 NM_000967.4 +GTSE1 ENST00000454366 NM_016426.7 +EIF4ENIF1 ENST00000330125 NM_019843.4 +SAMM50 ENST00000350028 NM_015380.5 +TTC38 ENST00000381031 NM_017931.4 +SLC25A17 ENST00000435456 NM_006358.4 +TRIOBP ENST00000644935 NM_001039141.3 +TTLL12 ENST00000216129 NM_015140.4 +PRR5 ENST00000336985 NM_181333.4 +PIM3 ENST00000360612 NM_001001852.4 +DENND6B ENST00000413817 NM_001001794.4 +CERK ENST00000216264 NM_022766.6 +PPP6R2 ENST00000612753 NM_001242898.2 +PRR14L ENST00000327423 NM_173566.3 +RTL6 ENST00000341255 NM_032287.3 +FAM83F ENST00000333407 NM_138435.4 +PVALB ENST00000417718 NM_001315532.2 +ALG12 ENST00000330817 NM_024105.4 +SYNGR1 ENST00000328933 NM_004711.5 +SEZ6L ENST00000248933 NM_021115.5 +IFT27 ENST00000433985 NM_001177701.3 +PDGFB ENST00000331163 NM_002608.4 +MPPED1 ENST00000443721 NM_001044370.2 +PARVG ENST00000444313 NM_022141.7 +BIK ENST00000216115 NM_001197.5 +TTLL1 ENST00000266254 NM_012263.5 +PKDREJ ENST00000253255 NM_006071.2 +ANKRD54 ENST00000215941 NM_138797.4 +TSPO ENST00000337554 NM_000714.6 +DNAJB7 ENST00000307221 NM_145174.2 +PATZ1 ENST00000266269 NM_014323.3 +SHISAL1 ENST00000381176 NM_001099294.2 +XPNPEP3 ENST00000357137 NM_022098.4 +ZNRF3 ENST00000544604 NM_001206998.2 +PACSIN2 ENST00000263246 NM_001184970.3 +RFPL3 ENST00000249007 NM_001098535.1 +RTCB ENST00000216038 NM_014306.5 +YWHAH ENST00000248975 NM_003405.4 +ASPHD2 ENST00000215906 NM_020437.5 +SRRD ENST00000215917 NM_001013694.3 +TFIP11 ENST00000407690 NM_012143.4 +CRYBB1 ENST00000647684 NM_001887.4 +CRYBA4 ENST00000354760 NM_001886.3 +C1QTNF6 ENST00000337843 NM_031910.4 +SSTR3 ENST00000610913 NM_001051.5 +TMPRSS6 ENST00000676104 NM_001374504.1 +SPECC1L ENST00000314328 NM_015330.6 +ADORA2A ENST00000337539 NM_000675.6 +UPB1 ENST00000326010 NM_016327.3 +SNRPD3 ENST00000215829 NM_004175.5 +LRRC75B ENST00000318753 NM_207644.3 +GGT1 ENST00000400382 NM_001288833.2 +TAFA5 ENST00000402357 NM_001082967.3 +MAPK1 ENST00000215832 NM_002745.5 +MTMR3 ENST00000401950 NM_021090.4 +MYO18B ENST00000335473 NM_032608.7 +SGSM3 ENST00000248929 NM_015705.6 +MORC2 ENST00000397641 NM_001303256.3 +DGCR6 ENST00000331444 NM_005675.6 +RRP7A ENST00000323013 NM_015703.5 +DNAL4 ENST00000216068 NM_005740.3 +NPTXR ENST00000333039 NM_014293.4 +CBX6 ENST00000407418 NM_014292.5 +APOBEC3B ENST00000333467 NM_004900.5 +APOBEC3C ENST00000361441 NM_014508.3 +APOBEC3F ENST00000308521 NM_145298.6 +APOBEC3G ENST00000407997 NM_021822.4 +TAB1 ENST00000216160 NM_006116.3 +MGAT3 ENST00000341184 NM_002409.5 +MIEF1 ENST00000325301 NM_019008.6 +RPS19BP1 ENST00000334678 NM_194326.4 +SLC25A18 ENST00000327451 NM_031481.3 +ATP6V1E1 ENST00000253413 NM_001696.4 +BCL2L13 ENST00000317582 NM_015367.4 +MICAL3 ENST00000441493 NM_015241.3 +ACR ENST00000216139 NM_001097.3 +TRMU ENST00000645190 NM_018006.5 +GRAMD4 ENST00000406902 NM_015124.5 +CELSR1 ENST00000674500 NM_001378328.1 +BID ENST00000622694 NM_001196.4 +CRELD2 ENST00000328268 NM_024324.5 +PARVB ENST00000338758 NM_013327.5 +ZC3H7B ENST00000352645 NM_017590.6 +TEF ENST00000266304 NM_003216.4 +TOB2 ENST00000327492 NM_016272.4 +PHF5A ENST00000216252 NM_032758.4 +POLR3H ENST00000355209 NM_001018050.4 +PMM1 ENST00000216259 NM_002676.3 +DESI1 ENST00000263256 NM_015704.3 +XRCC6 ENST00000360079 NM_001469.5 +SNU13 ENST00000401959 NM_001003796.2 +HSCB ENST00000216027 NM_172002.5 +COMT ENST00000361682 NM_000754.4 +ARVCF ENST00000263207 NM_001670.3 +TANGO2 ENST00000327374 NM_152906.7 +ZDHHC8 ENST00000334554 NM_013373.4 +CCDC188 ENST00000439765 NM_001365892.2 +HIRA ENST00000263208 NM_003325.4 +UFD1 ENST00000263202 NM_005659.7 +CDC45 ENST00000263201 NM_003504.5 +SEPTIN5 ENST00000455784 NM_002688.6 +GP1BB ENST00000366425 NM_000407.5 +GNB1L ENST00000329517 NM_053004.3 +RTN4R ENST00000043402 NM_023004.6 +DGCR6L ENST00000248879 NM_033257.4 +TXNRD2 ENST00000400521 NM_006440.5 +PANX2 ENST00000395842 NM_052839.4 +TRABD ENST00000380909 NM_001320485.2 +TUBGCP6 ENST00000248846 NM_020461.4 +HDAC10 ENST00000216271 NM_032019.6 +MAPK12 ENST00000215659 NM_002969.6 +MAPK11 ENST00000330651 NM_002751.7 +C22orf39 ENST00000399562 NM_173793.5 +MEI1 ENST00000401548 NM_152513.4 +TNFRSF13C ENST00000291232 NM_052945.4 +CENPM ENST00000215980 NM_024053.5 +WBP2NL ENST00000328823 NM_152613.3 +NAGA ENST00000396398 NM_000262.3 +PHETA2 ENST00000321753 NM_001002034.3 +CCDC134 ENST00000255784 NM_024821.5 +HMGXB4 ENST00000216106 NM_001003681.3 +MCM5 ENST00000216122 NM_006739.4 +HMOX1 ENST00000216117 NM_002133.3 +GUCD1 ENST00000435822 NM_001284254.2 +CACNG2 ENST00000300105 NM_006078.5 +SLC5A4 ENST00000266086 NM_014227.3 +LARGE1 ENST00000397394 NM_133642.5 +APOBEC3H ENST00000442487 NM_181773.5 +CIMIP4 ENST00000381821 NM_001163857.2 +MPST ENST00000429360 NM_021126.8 +C22orf23 ENST00000403305 NM_032561.5 +POLR2F ENST00000442738 NM_021974.5 +PICK1 ENST00000356976 NM_012407.4 +BAIAP2L2 ENST00000381669 NM_025045.6 +YDJC ENST00000292778 NM_001017964.2 +CCDC116 ENST00000292779 NM_152612.3 +SDF2L1 ENST00000248958 NM_022044.3 +PPIL2 ENST00000398831 NM_014337.4 +YPEL1 ENST00000339468 NM_013313.5 +ZNF74 ENST00000400451 NM_003426.4 +KLHL22 ENST00000328879 NM_032775.4 +GSTT2B ENST00000290765 NM_001080843.4 +DDTL ENST00000215770 NM_001084393.2 +CABIN1 ENST00000263119 NM_012295.4 +KREMEN1 ENST00000400335 NM_001039570.3 +EMID1 ENST00000334018 NM_133455.4 +RHBDD3 ENST00000216085 NM_012265.3 +RASL10A ENST00000216101 NM_006477.5 +NEFH ENST00000310624 NM_021076.4 +THOC5 ENST00000490103 NM_003678.5 +NIPSNAP1 ENST00000216121 NM_003634.4 +CABP7 ENST00000216144 NM_182527.3 +ZMAT5 ENST00000344318 NM_001003692.2 +UQCR10 ENST00000330029 NM_013387.4 +CASTOR1 ENST00000407689 NM_001037666.3 +TBC1D10A ENST00000215790 NM_031937.3 +SF3A1 ENST00000215793 NM_005877.6 +RNF215 ENST00000382363 NM_001017981.2 +SEC14L2 ENST00000615189 NM_012429.5 +MTFP1 ENST00000266263 NM_016498.5 +SEC14L3 ENST00000215812 NM_174975.5 +SEC14L4 ENST00000255858 NM_174977.4 +GAL3ST1 ENST00000406361 NM_001318104.2 +PES1 ENST00000354694 NM_014303.4 +DERL3 ENST00000318109 NM_001002862.3 +MIF ENST00000215754 NM_002415.2 +SUSD2 ENST00000358321 NM_019601.4 +TOM1 ENST00000449058 NM_005488.3 +TOMM22 ENST00000216034 NM_020243.5 +MLC1 ENST00000311597 NM_015166.4 +PLXNB2 ENST00000359337 NM_012401.4 +ESS2 ENST00000252137 NM_022719.3 +TSSK2 ENST00000399635 NM_053006.5 +GSC2 ENST00000086933 NM_005315.2 +SLC25A1 ENST00000215882 NM_005984.5 +TUBA8 ENST00000330423 NM_018943.3 +ADSL ENST00000623063 NM_000026.4 +RSPH14 ENST00000216036 NM_014433.3 +GNAZ ENST00000615612 NM_002073.4 +BCR ENST00000305877 NM_004327.4 +GCAT ENST00000248924 NM_014291.4 +GALR3 ENST00000249041 NM_003614.2 +EIF3L ENST00000652021 NM_016091.4 +MICALL1 ENST00000215957 NM_033386.4 +ACO2 ENST00000216254 NM_001098.3 +AP1B1 ENST00000357586 NM_001127.4 +MRPL40 ENST00000333130 NM_003776.4 +PRODH ENST00000357068 NM_016335.6 +APOBEC3D ENST00000216099 NM_152426.4 +PEX26 ENST00000399744 NM_001127649.3 +SERPIND1 ENST00000215727 NM_000185.4 +SNAP29 ENST00000215730 NM_004782.4 +CRKL ENST00000354336 NM_005207.4 +THAP7 ENST00000215742 NM_030573.3 +TCF20 ENST00000677622 NM_001378418.1 +APOL4 ENST00000683024 NM_001386885.1 +CECR2 ENST00000262608 NM_001290047.2 +AIFM3 ENST00000440238 NM_001386814.1 +LMF2 ENST00000474879 NM_033200.3 +NCAPH2 ENST00000420993 NM_152299.4 +SCO2 ENST00000395693 NM_005138.3 +TYMP ENST00000252029 NM_001953.5 +KLHDC7B ENST00000648057 NM_138433.5 +SYCE3 ENST00000406915 NM_001123225.3 +CPT1B ENST00000312108 NM_152246.3 +CHKB ENST00000406938 NM_005198.5 +MAPK8IP2 ENST00000329492 NM_012324.6 +ARSA ENST00000216124 NM_000487.6 +TMEM191C ENST00000536718 NM_001388354.1 +RAB36 ENST00000263116 NM_004914.5 +H1-0 ENST00000340857 NM_005318.4 +CLDN5 ENST00000618236 NM_001363066.2 +FAM227A ENST00000535113 NM_001013647.2 +RIMBP3C ENST00000433039 NM_001128633.2 +C22orf31 ENST00000216071 NM_015370.2 +PPM1F ENST00000263212 NM_014634.4 +TOP3B ENST00000357179 NM_001282112.2 +VPREB1 ENST00000403807 NM_007128.4 +CCDC157 ENST00000338306 NM_001017437.5 +CIMAP1B ENST00000329363 NM_001014440.4 +SHISA8 ENST00000621082 NM_001207020.3 +XKR3 ENST00000684488 NM_001386955.1 +JOSD1 ENST00000683374 NM_001360236.2 +SULT4A1 ENST00000330884 NM_014351.4 +PNPLA5 ENST00000216177 NM_138814.4 +MYH9 ENST00000216181 NM_002473.6 +RASD2 ENST00000216127 NM_014310.4 +MB ENST00000397326 NM_005368.3 +APOL6 ENST00000409652 NM_030641.4 +APOL5 ENST00000249044 NM_030642.1 +APOL2 ENST00000358502 NM_030882.4 +SEC14L6 ENST00000402034 NM_001193336.4 +LHFPL7 ENST00000640159 NM_001388199.1 +KIAA1671 ENST00000358431 NM_001145206.2 +CRYBB3 ENST00000215855 NM_004076.5 +CRYBB2 ENST00000398215 NM_000496.3 +ATF4 ENST00000674920 NM_182810.3 +CSF2RB ENST00000403662 NM_000395.3 +GRK3 ENST00000324198 NM_005160.4 +DMC1 ENST00000216024 NM_007068.4 +ST13 ENST00000216218 NM_003932.5 +SELENOO ENST00000380903 NM_031454.2 +SCUBE1 ENST00000360835 NM_173050.5 +SCARF2 ENST00000622235 NM_182895.5 +OR11H1 ENST00000643195 NM_001005239.2 +SLC2A11 ENST00000316185 NM_001024939.4 +GAB4 ENST00000400588 NM_001037814.1 +TTC28 ENST00000397906 NM_001145418.2 +GSTT4 ENST00000621179 NM_001358664.2 +BPIFC ENST00000300399 NM_174932.3 +KCTD17 ENST00000403888 NM_001282684.2 +ADM2 ENST00000395737 NM_001253845.2 +MIOX ENST00000216075 NM_017584.6 +SBF1 ENST00000380817 NM_002972.4 +RABL2B ENST00000691320 NM_001130919.3 +PPARA ENST00000407236 NM_005036.6 +CDPF1 ENST00000314567 NM_207327.5 +SERHL2 ENST00000327678 NM_014509.5 +ATP5MGL ENST00000505920 NM_001165877.1 +A4GALT ENST00000642412 NM_017436.7 +ARFGAP3 ENST00000263245 NM_014570.5 +CYB5R3 ENST00000352397 NM_000398.7 +TXN2 ENST00000216185 NM_012473.4 +FOXRED2 ENST00000397224 NM_001102371.2 +EIF3D ENST00000216190 NM_003753.4 +SUN2 ENST00000689035 NM_015374.3 +PIWIL3 ENST00000616349 NM_001255975.1 +BRD1 ENST00000404760 NM_001304808.3 +PISD ENST00000439502 NM_001326411.2 +RFPL2 ENST00000652607 NM_001394555.1 +P2RX6 ENST00000413302 NM_005446.5 +SLC16A8 ENST00000681075 NM_013356.3 +TMEM121B ENST00000331437 NM_031890.4 +IL17RA ENST00000319363 NM_014339.7 +HDHD5 ENST00000336737 NM_033070.3 +CBY1 ENST00000216029 NM_015373.4 +RBFOX2 ENST00000695854 NM_001349999.2 +GGT5 ENST00000327365 NM_004121.5 +IL17REL ENST00000695950 NM_001371417.1 +UBE2L3 ENST00000342192 NM_003347.4 +ADA2 ENST00000399837 NM_001282225.2 +IGLL1 ENST00000330377 NM_020070.4 +LRRC74B ENST00000442047 NM_001291006.2 +POLDIP3 ENST00000252115 NM_032311.5 +PI4KA ENST00000255882 NM_058004.4 +HIC2 ENST00000407464 NM_015094.3 +GRAP2 ENST00000344138 NM_004810.4 +TMA7B ENST00000424496 NM_001396013.1 +NFAM1 ENST00000329021 NM_145912.8 +ZNF280B ENST00000626650 NM_080764.4 +ZNF280A ENST00000302097 NM_080740.5 +PRAME ENST00000405655 NM_206956.3 +GGTLC2 ENST00000448514 NM_199127.3 +GTPBP1 ENST00000216044 NM_004286.5 +CHCHD10 ENST00000484558 NM_213720.3 +MMP11 ENST00000215743 NM_005940.5 +ASCC2 ENST00000307790 NM_032204.5 +L3MBTL2 ENST00000216237 NM_031488.5 +CHADL ENST00000216241 NM_138481.2 +SOX10 ENST00000396884 NM_006941.4 +MAFF ENST00000338483 NM_012323.4 +TMEM184B ENST00000361906 NM_012264.5 +CSNK1E ENST00000396832 NM_152221.3 +SLC35E4 ENST00000343605 NM_001001479.4 +DUSP18 ENST00000334679 NM_152511.5 +TCN2 ENST00000215838 NM_000355.4 +MCHR1 ENST00000249016 NM_005297.4 +TUG1 ENST00000644773 NM_001396518.1 +IL2RB ENST00000216223 NM_000878.5 +USP18 ENST00000215794 NM_017414.4 +HPS4 ENST00000398145 NM_022081.6 +GGA1 ENST00000343632 NM_013365.5 +SH3BP1 ENST00000649765 NM_018957.6 +LGALS1 ENST00000215909 NM_002305.4 +NOL12 ENST00000359114 NM_024313.3 +PLA2G6 ENST00000332509 NM_003560.4 +KCNJ4 ENST00000303592 NM_152868.3 +KDELR3 ENST00000216014 NM_006855.4 +DDX17 ENST00000403230 NM_006386.5 +TST ENST00000249042 NM_003312.6 +CYTH4 ENST00000248901 NM_013385.5 +ELFN2 ENST00000402918 NM_052906.5 +MFNG ENST00000356998 NM_002405.4 +CARD10 ENST00000251973 NM_014550.4 +CDC42EP1 ENST00000249014 NM_152243.3 +LGALS2 ENST00000215886 NM_006498.3 +TTLL8 ENST00000433387 NM_001350317.3 +RAC2 ENST00000249071 NM_002872.5 +APOL1 ENST00000397278 NM_003661.4 +GAS2L1 ENST00000616432 NM_001362985.3 +RIMBP3B ENST00000620804 NM_001128635.2 +FAM246A ENST00000652479 NM_001396025.1 +MRTFA ENST00000355630 NM_020831.6 +TBX1 ENST00000649276 NM_001379200.1 +LZTR1 ENST00000646124 NM_006767.4 +PITPNB ENST00000335272 NM_012399.5 +MN1 ENST00000302326 NM_002430.3 +RBX1 ENST00000216225 NM_014248.4 +EP300 ENST00000263253 NM_001429.4 +SMARCB1 ENST00000644036 NM_003073.5 +POTEH ENST00000343518 NM_001136213.1 +IGLL5 ENST00000526893 NM_001178126.2 +DDT ENST00000398344 NM_001084392.3 +TRMT2A ENST00000252136 NM_022727.6 +RANGAP1 ENST00000356244 NM_002883.4 +TPST2 ENST00000338754 NM_003595.5 +GGTLC3 ENST00000619998 NM_001355479.1 +RIMBP3 ENST00000619918 NM_015672.2 +FAM246B ENST00000652395 NM_001396026.1 +SLC7A4 ENST00000382932 NM_004173.3 +RGL4 ENST00000290691 NM_153615.2 +ZNF70 ENST00000341976 NM_021916.4 +VPREB3 ENST00000248948 NM_013378.3 +C22orf15 ENST00000402217 NM_182520.3 +EWSR1 ENST00000397938 NM_005243.4 +KIAA0930 ENST00000336156 NM_001009880.2 +UPK3A ENST00000216211 NM_006953.4 +FAM118A ENST00000441876 NM_017911.4 +SMC1B ENST00000357450 NM_148674.5 +RIBC2 ENST00000614167 NM_015653.5 +FBLN1 ENST00000327858 NM_006486.3 +CSDC2 ENST00000306149 NM_014460.4 +C22orf42 ENST00000382097 NM_001010859.3 +PDXP ENST00000215904 NM_020315.5 +CCDC117 ENST00000249064 NM_173510.4 +SGSM1 ENST00000400358 NM_001098497.3 +RFPL1 ENST00000354373 NM_021026.2 +CLTCL1 ENST00000427926 NM_007098.4 +DGCR8 ENST00000351989 NM_022720.7 +SMTN ENST00000333137 NM_134269.3 +SELENOM ENST00000400299 NM_080430.4 +INPP5J ENST00000331075 NM_001284285.2 +PLA2G3 ENST00000215885 NM_015715.5 +RNF185 ENST00000326132 NM_152267.4 +LIMK2 ENST00000331728 NM_005569.4 +PIK3IP1 ENST00000215912 NM_052880.5 +APOL3 ENST00000424878 NM_145639.2 +RTL10 ENST00000328554 NM_024627.6 +SEPTIN3 ENST00000644076 NM_001363845.2 +DEPDC5 ENST00000651528 NM_001242896.3 +SLC5A1 ENST00000266088 NM_000343.4 +FBXO7 ENST00000266087 NM_012179.4 +TIMP3 ENST00000266085 NM_000362.5 +SYN3 ENST00000358763 NM_003490.4 +DRICH1 ENST00000317749 NM_016449.4 +NUP50 ENST00000347635 NM_007172.4 +ATXN10 ENST00000252934 NM_013236.4 +WNT7B ENST00000339464 NM_058238.3 +APOBEC3A ENST00000249116 NM_145699.4 +NF2 ENST00000338641 NM_000268.4 +SREBF2 ENST00000361204 NM_004599.4 +MOV10L1 ENST00000262794 NM_018995.3 +CHEK2 ENST00000404276 NM_007194.4 +SMIM45 ENST00000381348 NM_001395940.1 +NDUFA6 ENST00000498737 NM_002490.6 +CYP2D6 ENST00000645361 NM_000106.6 +SMDT1 ENST00000331479 NM_033318.5 +RANBP1 ENST00000430524 NM_001278639.2 +ARHGAP8 ENST00000356099 NM_181335.3 +PHF21B ENST00000313237 NM_138415.5 +TMEM191B ENST00000612978 NM_001242313.1 +OSBP2 ENST00000332585 NM_030758.4 +DGCR2 ENST00000263196 NM_005137.3 +MIURF ENST00000637854 NM_001414695.1 +XBP1 ENST00000344347 NM_001079539.2 +PPP2R3B ENST00000390665 NM_013239.5 +PRKX ENST00000262848 NM_005044.5 +VCX2 ENST00000317103 NM_016378.3 +IL3RA ENST00000331035 NM_002183.4 +P2RY8 ENST00000381297 NM_178129.5 +SLC25A6 ENST00000381401 NM_001636.4 +AMELX ENST00000380714 NM_001142.2 +ASMT ENST00000381241 NM_001171038.2 +DHRSX ENST00000334651 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+TSPY4 ENST00000426950 NM_001164471.2 +TSPY8 ENST00000287721 NM_001243721.2 +TSPY3 ENST00000457222 NM_001077697.2 +ASPN ENST00000710274 NM_017680.6 +MUC2 ENST00000713550 NM_002457.5 +SHANK3 ENST00000710353 NM_001372044.2 +PRAMEF22 ENST00000713586 NM_001100631.2 +NBPF1 ENST00000713538 NM_001405666.3 +ENSG00000292227 ENST00000713540 NM_001405530.2 +OR8U8 ENST00000627176 NM_001013356.2 +OR8U9 ENST00000626074 NM_001013357.1 +OR9G9 ENST00000571130 NM_001013358.2 +OR4C45 ENST00000710319 NM_001005513.1 +FCGBP ENST00000628705 NM_003890.3 +MROH5 ENST00000707626 NM_207414.3 +POLR2A ENST00000643490 NM_000937.5 +CASP8AP2 ENST00000671703 NM_001137667.2 +SLC37A4 ENST00000642844 NM_001164277.2 +MUC16 ENST00000711671 NM_001401501.2 +GPATCH4 ENST00000710324 NM_001396855.1 +OR4Q2 ENST00000710368 NM_001348271.2 +OR11H7 ENST00000708727 NM_001348273.1 +ENSG00000292244 ENST00000710306 NM_001417890.1 +OR5AL1 ENST00000710330 NM_001348230.2 +IFNL4 ENST00000710321 NM_001276254.2 +VN1R5 ENST00000713554 NM_173858.1 +PNLIPRP2 ENST00000709157 NM_005396.5 +OR10J4 ENST00000710315 NM_001348286.3 +OR52E1 ENST00000710310 NM_001348221.2 +CD300H ENST00000709217 NM_001324073.3 +GBA3 ENST00000709220 NM_020973.5 +ZNF598 ENST00000710288 NM_178167.5 +MROH8 ENST00000710289 NM_152503.8 +FOXO6 ENST00000643531 NM_001291281.3 +CASP12 ENST00000709446 NM_001191016.3 +TAS2R45 ENST00000571573 NM_176886.2 +CCL3L3 ENST00000615140 NM_021006.6 +CCL4L2 ENST00000634014 NM_207007.4 +KIR2DL5B ENST00000611411 NM_001018081.2 +KIR2DL5A ENST00000613155 NM_020535.3 +KIR2DS5 ENST00000614053 NM_014513.3 +KIR2DS1 ENST00000621207 NM_014512.1 +FUT3 ENST00000709635 NM_001097639.3 +APOBEC3A ENST00000570508 NM_001193289.2 +GSTT2 ENST00000618279 NM_000854.5 +GSTT1 ENST00000612885 NM_000853.4 +GTF2H2C_2 ENST00000621406 NM_001354437.3 +HLA-DRB3 ENST00000383126 NM_022555.4 +HLA-DRB4 ENST00000457451 NM_021983.5 +C4B_2 ENST00000435500 NM_001242823.2 +UBE2NL ENST00000710304 NM_001012989.3 diff --git a/bin/add_annotations_cff.R b/bin/add_annotations_cff.R index bf22a75..e3628c7 100755 --- a/bin/add_annotations_cff.R +++ b/bin/add_annotations_cff.R @@ -11,7 +11,7 @@ suppressPackageStartupMessages({ usage <- function() { message("Usage:") - message("add_annotations_cff.R --cff-file --agfusion-file --oncokb-file --out-prefix --transcripts ") + message("add_annotations_cff.R --cff-file --agfusion-file --oncokb-file --out-prefix ") } args = commandArgs(TRUE) @@ -39,14 +39,14 @@ parse_args <- function(x){ args_opt <- parse_args(paste(args,collapse=" ")) -possible_args = c("cff", "oncokb", "agfusion", "out_prefix","transcripts") +possible_args = c("cff", "oncokb", "agfusion", "out_prefix") if (length(setdiff(names(args_opt),possible_args)) > 0){ message("Invalid options") usage() quit() } -required_args <- c("cff","agfusion","out_prefix","transcripts") +required_args <- c("cff","agfusion","out_prefix") if (length(setdiff(required_args,names(args_opt))) > 0) { message("Missing required arguments") usage() @@ -57,14 +57,11 @@ oncokb_file = args_opt$oncokb agfusion_file = args_opt$agfusion cff_file = args_opt$cff out_prefix = args_opt$out_prefix -transcripts = args_opt$transcripts cff = fread(cff_file) final_cff_cols <- c(names(cff)) agfusion_tab = fread(agfusion_file) %>% select(c(`5'_transcript`,`3'_transcript`,`5'_breakpoint`,`3'_breakpoint`,Fusion_effect)) -#Add transcript version corresponding to gtf ensembl version -transcripts <- read.delim(transcripts,header = F) -transcripts <- transcripts[,c("V15","V16")] + final_cff_cols <- c(final_cff_cols,"Fusion_effect") @@ -89,26 +86,6 @@ cff <- merge( all.x = T, all.y = T ) -### merge -cff <- merge( - cff, - transcripts, - by.x = "gene3_transcript_id", - by.y = "V15", - all.x = T , - all.y = F) -cff$gene3_transcript_id <- ifelse(is.na(cff$gene3_transcript_id),NA,paste0(cff$gene3_transcript_id,".",cff$V16)) -cff$V16 <- NULL -cff <- merge( - cff, - transcripts, - by.x = "gene5_transcript_id", - by.y = "V15", - all.x = T, - all.y = F) - -cff$gene5_transcript_id <- ifelse(is.na(cff$gene5_transcript_id),NA,paste0(cff$gene5_transcript_id,".",cff$V16)) -cff$V16 <- NULL cff <- as.data.frame(cff)[,c(final_cff_cols)] #cff <- cff %>% mutate(!!final_cff_cols[34] := Fusion_effect) %>% select(-c(Fusion_effect)) diff --git a/conf/igenomes.config b/conf/igenomes.config index 9b229f7..bf599d9 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -33,7 +33,6 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37/blocklist_breakpoints.bedpe.gz" clinicalgenes = "${projectDir}/assets/clinical_allowlist_hg19.txt" ensembl_version = 75 - transcripts = "https://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_core_75_37/transcript.txt.gz" } 'GRCh38' { ensembl_version = 111 @@ -45,6 +44,7 @@ params { starfusion_url = "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz" cdna = "https://ftp.ensembl.org/pub/release-111/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz" metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh38/blocklist_breakpoints.hg38.bedpe.gz" + clinicalgenes = "${projectDir}/assets/mane_v1.2_allowlist.txt" baits { 'idt_v2' { targets = "/juno/work/ccs/cmopipeline/forte/GRCh38_probes/xgen-exome-hyb-panel-v2-targets-hg38.bed" diff --git a/modules/local/cff_annotate/main.nf b/modules/local/cff_annotate/main.nf index c2d2e31..4a81bcf 100644 --- a/modules/local/cff_annotate/main.nf +++ b/modules/local/cff_annotate/main.nf @@ -8,7 +8,6 @@ process CFF_ANNOTATE { input: tuple val(meta), path(cff), path(oncokb), path(agfusion) - path(transcripts) output: tuple val(meta), path("${prefix}.unfiltered.cff"), emit: unfiltered_cff @@ -26,8 +25,7 @@ process CFF_ANNOTATE { --cff ${cff} \\ ${oncokb_param} \\ --agfusion ${agfusion} \\ - --out-prefix ${prefix} \\ - --transcripts ${transcripts} + --out-prefix ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf index 20cbfa0..892bb33 100644 --- a/subworkflows/local/fusion.nf +++ b/subworkflows/local/fusion.nf @@ -142,8 +142,7 @@ workflow FUSION { CFF_FINALIZE( ADD_FLAG.out.unfiltered_cff .join(ONCOKB_FUSIONANNOTATOR.out.oncokb_fusions, by:0) - .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0), - transcripts + .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0) ) } else { CFF_FINALIZE( @@ -151,8 +150,7 @@ workflow FUSION { .join(AGFUSION_BATCH.out.fusion_transcripts_tsv, by:0) .map{ meta, cff, agfusion_file -> [ meta, cff, [], agfusion_file ] - }, - transcripts + } ) } ch_versions = ch_versions.mix(ADD_FLAG.out.versions.first()) diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf index 4ead812..e0c816a 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references.nf @@ -105,7 +105,7 @@ workflow PREPARE_REFERENCES { //cosmic_passwd = params.cosmic_passwd ?: "" AGAT_SPADDINTRONS( - [[id:params.ensembl_version],gtf], + gtf, [] ) From 9d05254a99d48516efb7e38660c4b66501eadf1d Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 6 Nov 2024 16:16:22 -0500 Subject: [PATCH 37/39] whitespace --- modules/local/cff_annotate/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/cff_annotate/main.nf b/modules/local/cff_annotate/main.nf index 4a81bcf..6a438b4 100644 --- a/modules/local/cff_annotate/main.nf +++ b/modules/local/cff_annotate/main.nf @@ -25,7 +25,7 @@ process CFF_ANNOTATE { --cff ${cff} \\ ${oncokb_param} \\ --agfusion ${agfusion} \\ - --out-prefix ${prefix} + --out-prefix ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": From 38927ceb933cfab916b6bc5c8d65f12a068efefe Mon Sep 17 00:00:00 2001 From: Alexandria Pinto Date: Wed, 13 Nov 2024 12:49:10 -0500 Subject: [PATCH 38/39] remove instances of transcript version --- conf/igenomes.config | 1 - main.nf | 1 - 2 files changed, 2 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index bf599d9..8a65810 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -61,7 +61,6 @@ params { metafusion_blocklist = "https://raw.githubusercontent.com/anoronh4/forte-references/main/GRCh37_test/blocklist_breakpoints.bedpe" ensembl_version = 75 clinicalgenes = "${projectDir}/assets/clinical_allowlist_hg19.txt" - transcripts = "https://ftp.ensembl.org/pub/release-75/mysql/homo_sapiens_core_75_37/transcript.txt.gz" } /* 'hg38' { diff --git a/main.nf b/main.nf index de37dd9..8714d17 100644 --- a/main.nf +++ b/main.nf @@ -29,7 +29,6 @@ params.metafusion_gene_bed = WorkflowMain.getGenomeAttribute(params, 'metafus params.metafusion_gene_info = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_info') params.ensembl_version = WorkflowMain.getGenomeAttribute(params, 'ensembl_version') params.clinicalgenes = WorkflowMain.getGenomeAttribute(params, 'clinicalgenes') -params.transcripts = WorkflowMain.getGenomeAttribute(params, 'transcripts') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 78b11bfa16b86dbd9ba5df88de9f8718504f173e Mon Sep 17 00:00:00 2001 From: pintoa1-mskcc <90696363+pintoa1-mskcc@users.noreply.github.com> Date: Fri, 15 Nov 2024 16:09:33 -0500 Subject: [PATCH 39/39] remove transcripts file, no longer implementing --- subworkflows/local/fusion.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/fusion.nf b/subworkflows/local/fusion.nf index 892bb33..ab69dc5 100644 --- a/subworkflows/local/fusion.nf +++ b/subworkflows/local/fusion.nf @@ -38,7 +38,6 @@ workflow FUSION { //gene_bed = params.metafusion_gene_bed clinicalgenes = params.clinicalgenes //blocklist = params.metafusion_blocklist - transcripts = params.transcripts STAR_FOR_ARRIBA( reads,