biopipen 0.33.1__py3-none-any.whl → 0.34.1__py3-none-any.whl

{biopipen-0.33.1.dist-info → biopipen-0.34.1.dist-info}/RECORD

@@ -1,37 +1,37 @@
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 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
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 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biopipen/ns/bed.py,sha256=EqpSa7Hx6GImvJNghtV4uDo2PnPXeUt1Yq9AFWJP9_8,8159
 biopipen/ns/cellranger.py,sha256=rZKE3eHbxMrUzw3XJihAYOuq07OA6fmvbnJcwdHiLzs,5876
 biopipen/ns/cellranger_pipeline.py,sha256=IjCCGpr1HB3R4nRyBcAgWmF0HsLYmHd6nGMn2-wkWOM,4075
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 biopipen/ns/cnvkit_pipeline.py,sha256=Nlg4VLHV3iGKwFaXtVOyC-j4foI6GOUFbw2SgPs1KvQ,37162
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 biopipen/ns/gene.py,sha256=rty-Bjcf87v2vyb9X4kRvfrQ6XQYXgN4f2ftFO0nWA8,3888
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 biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
 biopipen/ns/regulatory.py,sha256=gJjGVpJrdv-rg2t5UjK4AGuvtLNymaNYNvoD8PhlbvE,15929
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
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 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
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 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
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 biopipen/ns/vcf.py,sha256=zjOH2qiSJsHACLmBqV-Tew-mn-peZgvYLAWjTLh7uTI,23823
 biopipen/ns/web.py,sha256=8VY4Xsb8UrzS4IkGUX_84GQP1JG6NcTZrV7f9tA1tUI,5458
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
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 biopipen/reports/bam/ControlFREEC.svelte,sha256=OwN96RW0dN-gtQ1zWKbXYZCYkkrOC0RQmP3UG4x7zqU,837
 biopipen/reports/cellranger/CellRangerCount.svelte,sha256=InkkGold9Vta8vSPeE7WgFuFWuMVBkQvwc2yxWFGVM4,466
 biopipen/reports/cellranger/CellRangerSummary.svelte,sha256=WEYPwmcmgtSqpFpTvNPV40yZR-7ERa5LgZni2RXxUZQ,348
@@ -39,34 +39,28 @@ biopipen/reports/cellranger/CellRangerVdj.svelte,sha256=InkkGold9Vta8vSPeE7WgFuF
 biopipen/reports/cnv/AneuploidyScore.svelte,sha256=x0LbhqjauZpqMzmzDWmYgx-rEh5Tzo8qBrXcLcM0h78,1020
 biopipen/reports/cnv/AneuploidyScoreSummary.svelte,sha256=AWlns70mChJGhH3z8r5uXuI4tc7VbVN_cOUdqBr3ZKg,4414
 biopipen/reports/cnv/TMADScoreSummary.svelte,sha256=tJutaMOqeXxKroAosOIqOJVyhTTFet-soMwuOYVHTYU,2060
-biopipen/reports/cnvkit/CNVkitDiagram.svelte,sha256=8QLihBVH8RaHtjOUTU7xh4CCmFyxO1Bb9oOvLkOHeVo,467
-biopipen/reports/cnvkit/CNVkitHeatmap.svelte,sha256=IhwSvEdx3h-LZuwKN3vgiUIW8MD7a280YXqL_xNvIOA,519
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-biopipen/reports/delim/SampleInfo.svelte,sha256=Vpjrdd3AXNDNhx2pzDaFA61xPMYAFKvvIoVCqUswiyo,365
+biopipen/reports/cnvkit/CNVkitDiagram.svelte,sha256=qEX5EscFuRqmhrKrF_rwRkxyc4ocakAzo8j2eP0zLN4,455
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 biopipen/reports/gsea/FGSEA.svelte,sha256=3gNbZovmRWK6QjtxfgZgmft6LUurVZfQyHBRqyGMosk,405
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 biopipen/reports/protein/ProdigySummary.svelte,sha256=WEYPwmcmgtSqpFpTvNPV40yZR-7ERa5LgZni2RXxUZQ,348
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 biopipen/reports/scrna/CellsDistribution.svelte,sha256=Mg6P0tazpzOxsOAtc-0LGEim5KprPt5KIgoW3TzrxxA,413
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 biopipen/reports/tcr/ClonalStats.svelte,sha256=yxSzrEGYiq9pcAZRtSCuHB4KOq4A1I-sXJ73Wb4OEBQ,367
 biopipen/reports/tcr/CloneResidency.svelte,sha256=pzjkdGAhB7STxlXkTY5wnTT3plhkAPKMdGa6jwKuwoc,470
 biopipen/reports/tcr/Immunarch.svelte,sha256=jHOGUCWREaDNUf1_s6h9Kx_sp-y_dDRqY1rWrx0o0LM,433
@@ -74,7 +68,6 @@ biopipen/reports/tcr/SampleDiversity.svelte,sha256=GrPUpQ6aJPtyQHoFL9ayG6knpW6yZ
 biopipen/reports/tcr/TCRClusterStats.svelte,sha256=YGK5_Vp85QmUJZO1ZGtg1IWBsh9o-z-dSYC8kuW3ssU,415
 biopipen/reports/tcr/TESSA.svelte,sha256=S1tG0HIU5569ybV0shuTz1CN0JcqFrFNB7M6JCiGhm0,1948
 biopipen/reports/tcr/VJUsage.svelte,sha256=c9G2-APGG0l-c6b32aFOimrP_QYD-oELBASN4VabXmk,426
-biopipen/reports/utils/gsea.liq,sha256=5uxNPyIr0xd7nrZePJlIsRyqCPx1uVWso7ehE1F-C4k,3556
 biopipen/reports/utils/misc.liq,sha256=hj9x4-vqPmVu0ZqoYeHqxanAmHHAlAySZ76YP0vFMEk,2146
 biopipen/reports/vcf/TruvariBenchSummary.svelte,sha256=yew8HRN-YahBzX504Micah5BTnoL_PQzQfN_87TiuOA,577
 biopipen/reports/vcf/TruvariConsistency.svelte,sha256=BBvtxi1EPmGH7j5M5zMOcLEhKWZOlKoXp1lrQGAmz_0,647
@@ -83,9 +76,10 @@ biopipen/scripts/bam/BamSampling.py,sha256=OzR3bRak3mqMF_7gHVCmdP9IinBxdUh5Ei8zF
 biopipen/scripts/bam/BamSort.py,sha256=vCFWR0asRDhFFbWm-nZJPi4lwfwNtsANa9DB4CjzyrY,5112
 biopipen/scripts/bam/BamSplitChroms.py,sha256=TFIiX9NnvcHzRuOIhqNMiRZ5Dc64X6P7WGj1qz5ihlU,4995
 biopipen/scripts/bam/BamSubsetByBed.py,sha256=98M-oynqCTR_4afRASfM6CSN3-JG2kRnl6P5PVR3zdc,1030
-biopipen/scripts/bam/CNAClinic.R,sha256=mQXwtShL54HZXGCPqgPKPrU74_6K_8PqtOtG0mgA-F0,5062
-biopipen/scripts/bam/CNVpytor.py,sha256=HItxRw9vMTrB9ooOp88Syus4pY0jUZ8ZgcA2WKNqeAk,18055
-biopipen/scripts/bam/ControlFREEC.py,sha256=mopG1bnFjR412MEVdP5aoLhJrUTuxZuOUjzjYazMUPY,3337
+biopipen/scripts/bam/CNAClinic.R,sha256=hpTh-JeIDCYEN56bxJdCqq1yK4ap0_H072kCkxBpDdM,6318
+biopipen/scripts/bam/CNVpytor.py,sha256=zUWkXHlFRzpGiPzY5kMlfEze_AUDB14VgZim_GJvfH0,18096
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+biopipen/scripts/bam/SamtoolsView.py,sha256=LbZcS3nhDLZPF2kvap24L48k61nPiwTXJ0IILVyf1Fk,967
 biopipen/scripts/bed/Bed2Vcf.py,sha256=CyFzfHSau2ntgPHo4nSaaeRZbaXpbBoW8YmPxxWJQlc,5128
 biopipen/scripts/bed/BedConsensus.py,sha256=dgWEWCBX2cnZhxzJCF3WD8_JqlDAyPIDZlJ0Qiws0VA,2449
 biopipen/scripts/bed/BedLiftOver.sh,sha256=gTIYN_KnNtPxKTjGdk4EYhwQ-kgPN5rO5YVvG6kxB0k,327
@@ -95,10 +89,10 @@ biopipen/scripts/bed/BedtoolsMerge.py,sha256=d20obKLaJQALDNQ-Jz--OiL8klHGN44octk
 biopipen/scripts/cellranger/CellRangerCount.py,sha256=Te_tscWv_r2oTKPezN0zAkfuoQ3wwNqZC1IrsXjySYk,3307
 biopipen/scripts/cellranger/CellRangerSummary.R,sha256=eLcgU3b2HdK0AaKNz1-B14atptJTsJFpr2W-VYx1C18,10788
 biopipen/scripts/cellranger/CellRangerVdj.py,sha256=APatSSEjRdOYF2lF-kafJACtvR8l8UlvKJQDtn9Gk18,2287
-biopipen/scripts/cnv/AneuploidyScore.R,sha256=Bpm1cU7VkoinoKKzMuzqFntS8hjdd2IpBUjDiZyM7l4,9163
-biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=dSnekzXetM8BDmZPhHOS8WwEeOfszPfqthq6TrZ3aPc,12452
-biopipen/scripts/cnv/TMADScore.R,sha256=IH07REfBO3QB2QNWuwGY6LgAUAOE0lsfP6W0bS67zGs,1530
-biopipen/scripts/cnv/TMADScoreSummary.R,sha256=w58LD5xHnLal9jv53nBUGpQ8eTkAyEk1leCVN2T_ZaM,7109
+biopipen/scripts/cnv/AneuploidyScore.R,sha256=b8B3uT8drOPxTWMFKU0BgVxtc8xTq8SD00dJWwoHxrE,9287
+biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=cj9pEFOry-yKET0H6-_PQsAy1Rgp0KCEPqXq6_V1cgY,12322
+biopipen/scripts/cnv/TMADScore.R,sha256=xQ3qImpbgVafXNP2bbCZQ6dZ6YTKFpcrUbM7su2PKfs,1514
+biopipen/scripts/cnv/TMADScoreSummary.R,sha256=zeusC4yWXS3XBspNuFe6jh_facJfgpjKTK_wjI5wUwI,5165
 biopipen/scripts/cnvkit/CNVkitAccess.py,sha256=QWYPeXx9jaOg8ldKlAAtH6GS4X64FO4ajU1cfOAYS4s,762
 biopipen/scripts/cnvkit/CNVkitAutobin.py,sha256=GdpWg_7NQwENU8Q_I1Mm6hngeyLEGdBEQL6TcFrwwPg,1975
 biopipen/scripts/cnvkit/CNVkitBatch.py,sha256=3P7mcGDaqL4L6gO6oH6NOj46bCCCM6S9AqVYSJ50rF4,3828
@@ -106,21 +100,22 @@ biopipen/scripts/cnvkit/CNVkitCall.py,sha256=YSdOzsatvQHSNQj6C0mZWHAlc2xkQQOns9D
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 biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
 biopipen/scripts/tcr/Attach2Seurat.R,sha256=0KZaBkuPvqOBXq4ZG3pzIIua5HL-161K5dVXRoCysy4,1366
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-biopipen/scripts/tcr/CloneResidency.R,sha256=RbQT81wVsh8N6YTT4BrAl6dbcQG7obDqI9-fEq_fYwk,22033
-biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=hds1C80Q_W40Ikp-BrFfvh_aBf_V61lz-1YAvkDESyk,4569
+biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=vU-5sjFZktSzBBj4f1frIGChOV8P8Uf0mMWS2Njdsww,15204
+biopipen/scripts/tcr/ClonalStats.R,sha256=skqPMTHL8zMGIZ2Q_gKXm9UDFRR-wFRurtrmvbQp7pg,29340
+biopipen/scripts/tcr/CloneResidency.R,sha256=3pong__cdn2bW7pctq4TLcEdcj_xNigzyKnznnmc1i8,22021
+biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=zw5WPgq_lbfdDb9Ou07boh9D2FYjXZtCQKZCP0PKMYw,4561
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=jo0d58K57CF4W6mc2Q-hQn9rLl6oLHTsr5JceP8xqN0,54874
 biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=X_iXdgKZ9V5T87jXBdml0H6bwiDjsAqoPKhsdF72lj8,53904
 biopipen/scripts/tcr/GIANA/Imgt_Human_TRBV.fasta,sha256=XUwDPXJxVH5O9Q0gCL6EILKXEwVyiAZXm4VS2vkPcnQ,15371
@@ -237,16 +230,17 @@ biopipen/scripts/tcr/Immunarch-spectratyping.R,sha256=dR4p8NkJbtaF2JNyKbVrBofItj
 biopipen/scripts/tcr/Immunarch-tracking.R,sha256=LnqNRn77LDi1IKH_2CT5-w4-d4lhYqLV1SSVP7X-Wk4,4582
 biopipen/scripts/tcr/Immunarch-vjjunc.R,sha256=HzEwAVZ6yc8mIE5Q5G42SAwj-VKxAIrFICUPv3PQ5GA,5772
 biopipen/scripts/tcr/Immunarch.R,sha256=MvkWbSYeevZAtyjrztWm6Kaw58SZqK_HpPyrL9JYq1k,4804
-biopipen/scripts/tcr/Immunarch2VDJtools.R,sha256=QB9ILGbnsfoWaRANK6ceb14wpSWy8F1V1EdEmfIqiks,706
-biopipen/scripts/tcr/ImmunarchFilter.R,sha256=xVuBa38SPQ7qSSynDwvyuYljs1M0yKaIhCQ2eWE3vOc,3995
-biopipen/scripts/tcr/ImmunarchLoading.R,sha256=Vw2oIza3mDJzg9kuo-w5jvwdivk4AtDA6oF1RG1Sva8,5776
+biopipen/scripts/tcr/Immunarch2VDJtools.R,sha256=F9y_qABSMy8Dv3T0wy0_wxBJE19q4oq6xSG_sqSkVvs,698
+biopipen/scripts/tcr/ImmunarchFilter.R,sha256=-en-zi0ZB1JjuqhPlaEAN8YvHrELZNJ1V7NhRjB3Ghw,3983
+biopipen/scripts/tcr/ImmunarchLoading.R,sha256=u3o2aag_7cZ17HA8RxpN58wvrII0Uh-q6FY6dA8MWeQ,5756
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
-biopipen/scripts/tcr/ScRepLoading.R,sha256=WvmZuudav0BAAWe8-m7BVb3KsOIS0o2QSfARMobiG6A,4654
-biopipen/scripts/tcr/TCRClusterStats.R,sha256=gW1Xhd_yw5H3QgmO3R-ktKhpJZavyWh2zi-PrGq9nQA,13538
-biopipen/scripts/tcr/TCRClustering.R,sha256=Lt_e32c52gJ9fz1abboGXLIR--Lx2dqW0oFlSOCrCVs,10079
+biopipen/scripts/tcr/ScRepCombiningExpression.R,sha256=IJ7wHFKL5STWPv-mtWWt1-Ly_Evei146U0y0ZB9jCGE,933
+biopipen/scripts/tcr/ScRepLoading.R,sha256=eqJXTXn_HyLRo98Hv6xI_AmYp5l2LxHsyrMSXWZ_HmM,5167
+biopipen/scripts/tcr/TCRClusterStats.R,sha256=ns3S95DVDBuhSe1YgTZ1OksbfBgREO2Tnp1d4QzbTw0,13530
+biopipen/scripts/tcr/TCRClustering.R,sha256=b-IZeE3Rcue4Ntn9H7FLljELzycbWCyKP17LlBCuMW0,9658
 biopipen/scripts/tcr/TCRDock.py,sha256=Oyw27k6vr0pnJ0w1-lrk5b6sZ_IOf6TmbhSxQae-3Q8,3148
-biopipen/scripts/tcr/TESSA.R,sha256=XiAWCLjvzmrb6t0zGybNsRGK9LC-esgNY30ZlycSwS0,7022
+biopipen/scripts/tcr/TESSA.R,sha256=FRymeD9xYScKEMbl_OjW_sbEvQmTpXRqHaAFQaCBm1k,5756
 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
 biopipen/scripts/tcr/TESSA_source/BriseisEncoder.py,sha256=z4_Q_6StymffuUGGjHP1-B3aTsXtamKao5Q1-Kg9has,6831
 biopipen/scripts/tcr/TESSA_source/MCMC_control.R,sha256=93Nnz0IG8KfFnVscZDvmBp1qccZoSoG_jIVpOWBQLHE,2911
@@ -257,7 +251,7 @@ biopipen/scripts/tcr/TESSA_source/post_analysis.R,sha256=6RX7gdqd1N7lQVfwJBgjfEZ
 biopipen/scripts/tcr/TESSA_source/real_data.R,sha256=tg3BbiTpRVQWBRZStnzkC2jI1PCmxUA0fjWK09J6grw,2448
 biopipen/scripts/tcr/TESSA_source/update.R,sha256=kVrf6zgIkhhiQ2O55XGmxm_DGBKSpcShFgkyPNQIet0,6661
 biopipen/scripts/tcr/TESSA_source/utility.R,sha256=6qbkMV7yp4bgQe718QiASQUAgOE2euiLgAXOeSqrvHQ,374
-biopipen/scripts/tcr/VJUsage.R,sha256=LjHEbAHW3WriCYiM9-T6Esd4jc6pnoiSxBKTN_YA490,437
+biopipen/scripts/tcr/VJUsage.R,sha256=2ad9758GRqwVHdxyTd5e80u7vkk8ndGFyL2r5P0aRFE,417
 biopipen/scripts/tcr/immunarch-patched.R,sha256=6OAaV6arDVSI409VHuh1oMCuxlMQp-EaM-kkF-sTlCI,7007
 biopipen/scripts/tcr/vdjtools-patch.sh,sha256=-gJFPVqzzFLdet3q2hccB8gSztRawLV1AnqNp1ZzHOg,568
 biopipen/scripts/vcf/BcftoolsAnnotate.py,sha256=12-VUSP0kl0iyxvahhiu1CDyYJ9nTgGo5RWWVKhkBN8,2615
@@ -266,7 +260,7 @@ biopipen/scripts/vcf/BcftoolsMerge.py,sha256=KpCcEKNtDOEn8n0qSyWpi-lFv1qjnwqJRUl
 biopipen/scripts/vcf/BcftoolsSort.py,sha256=Gq7d3q7B-YFWw9wE9AO-nL_T5RDckSj-8oCcbsv3yq8,3799
 biopipen/scripts/vcf/BcftoolsView.py,sha256=tFOXskcR3gH576WZNvDcfjBLuzdAztdD1AnxmRTFUA4,2490
 biopipen/scripts/vcf/TruvariBench.sh,sha256=5M7lZhO4laNJvCVCHudf8DYArKNXoiPWuSkXgRi2t_A,908
-biopipen/scripts/vcf/TruvariBenchSummary.R,sha256=rdNNIPoiwqnK6oEOlQUUhnL1MF958W_nDjRCkA5ubz4,1516
+biopipen/scripts/vcf/TruvariBenchSummary.R,sha256=1mL32V1WoZ5a_QWx3D9sm_DpRqZjp9bKRqz91I6j2lg,1475
 biopipen/scripts/vcf/TruvariConsistency.R,sha256=6h20v8qztbl1KZInJwoSK_t5XwqhKMTMzPWNPhoAjlM,2314
 biopipen/scripts/vcf/Vcf2Bed.py,sha256=E0Bu7uqKhCPoikD_hM9dgNtzrjgZPQiPPSruULAlz4E,879
 biopipen/scripts/vcf/VcfAnno.py,sha256=cxLVTmJ-U2zlz3dUys2xzdQ6oXaHNOZY6AlHGynyZv4,1003
@@ -285,22 +279,13 @@ biopipen/scripts/web/GCloudStorageDownloadBucket.py,sha256=EnjEnCL52-X8v8d5tMvhJ
 biopipen/scripts/web/GCloudStorageDownloadFile.py,sha256=2txA7W0AfnnuyocZtLp20I-RFAF2dCbL8sL7NzKkiyI,839
 biopipen/scripts/web/gcloud_common.py,sha256=rMa42CRw3iJGV1OnG8A2KqLWFp8BocCH2nXRgkNSh1A,1254
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+biopipen/utils/common_docstrs.py,sha256=tz3h1Uj6_plAT08DGpYi661JIkBmnwHXpatdqbKjeEc,6470
 biopipen/utils/gene.py,sha256=ToRgAPYc8E72Hm6uYi84ImQaRMPZp5rN7O4CxK7vCag,4477
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 biopipen/utils/reference.py,sha256=Oc6IlA1giLxymAuI7DO-IQLHQ7-DbsWzOQE86oTDfMU,5955
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 biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
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{biopipen-0.33.1.dist-info → biopipen-0.34.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.1
+Generator: poetry-core 2.1.3
 Root-Is-Purelib: true
 Tag: py3-none-any

biopipen/reports/scrna/CellCellCommunicationPlots.svelte

@@ -1,14 +0,0 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
-<script>
-    import { Image } from "$libs";
-</script>
-
-{%- macro report_job(job, h=1) -%}
-    {{ job | render_job: h=h }}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-    <h1>{{job.in.cccfile | stem0 | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/ScFGSEA.svelte

@@ -1,16 +0,0 @@
-{% from "utils/gsea.liq" import fgsea_report -%}
-{% from "utils/misc.liq" import report_jobs -%}
-<script>
-    import { Image, DataTable, Descr } from "$libs";
-    import { Accordion, AccordionItem, Tabs, Tab, TabContent, InlineNotification } from "$ccs";
-</script>
-
-{%- macro report_job(job, h=1) -%}
-    {{ job | render_job: h=h }}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-    <h1>{{job.in.srtobj | stem0 | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/SeuratClusterStats.svelte

@@ -1,16 +0,0 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
-{% from_ os import path %}
-<script>
-    import { DataTable, Image, Descr, Plotly } from "$libs";
-    import { Tabs, Tab, TabContent } from "$ccs";
-</script>
-
-{%- macro report_job(job, h=1) -%}
-    {{ job | render_job: h=h }}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-    <h1>{{job.in.srtobj | stem}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/SeuratMap2Ref.svelte

@@ -1,37 +0,0 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
-<script>
-    import { Image, DataTable } from "$libs";
-</script>
-
-{%- macro report_job(job, h=1) -%}
-
-<h{{h}}>UMAPs</h{{h}}>
-{% set imgs = [] %}
-{% set caps = [] %}
-{% for png in job.outdir | glob: "UMAPs-*.png" %}
-    {% set pdf = png | regex_replace: "\\.png$", ".pdf" %}
-    {% set stm = png | stem %}
-    {% set _ = imgs.append({"src": png, "download": pdf}) %}
-    {% set _ = caps.append(stm | replace: "UMAPs-", "") %}
-{% endfor %}
-{{ table_of_images(imgs, caps) }}
-
-<h{{h}}>Mapping Score</h{{h}}>
-<Image
-    src="{{job.outdir | joinpath: 'mapping_score.png'}}"
-    download="{{job.outdir | joinpath: 'mapping_score.pdf'}}"
-    />
-
-<h{{h}}>Stats</h{{h}}>
-{% for stfile in job.outdir | glob: "stats-*.txt" %}
-    <h{{h+1}}>{{stfile | stem | replace: "stats-", ""}}</h{{h+1}}>
-    <DataTable src="{{stfile}}" data={ {{stfile | datatable: sep="\t"}} } />
-{% endfor %}
-
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-<h1>{{job.in.sobjfile | stem0 | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/SeuratPreparing.svelte

@@ -1,15 +0,0 @@
-{% from "utils/misc.liq" import report_jobs -%}
-{% from_ os import path %}
-<script>
-    import { Image, DataTable, Descr } from "$libs";
-</script>
-
-{%- macro report_job(job, h=1) -%}
-    {{ job | render_job: h=h }}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-    <h1>{{job.in.metafile | stem}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte

@@ -1,28 +0,0 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
-{% from "utils/gsea.liq" import fgsea_report, gsea_report -%}
-
-<script>
-  import { Image, DataTable, Descr } from "$libs";
-  import { Tabs, Tab, TabContent, Accordion, AccordionItem, InlineNotification } from "$ccs";
-</script>
-
-{%- macro report_job(job, h=2) -%}
-  {% if envs.fgsea %}
-    {{ job | render_job: h=h }}
-  {% else %}
-    {%  for groupdir in job.out.outdir | glob: "*" %}
-      <h{{h}}>{{groupdir | basename}}</h{{h}}>
-      {%- set dsdirs = groupdir | glob: "*" -%}
-      {% for dsdir in groupdir | glob: "*" %}
-          <h{{h+1}}>{{ dsdir | basename }}</h{{h+1}}>
-          {{ gsea_report(dsdir, h+2, envs, envs.top) }}
-      {% endfor %}
-    {% endfor %}
-  {% endif %}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-  <h1>{{job.in.sobjfile | stem | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}