From 5cf9dcf15c3e384d02b81e81cb3e2c4a1de0efa4 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 7 Dec 2020 16:30:53 +1100 Subject: first draft --- autogen.pdf | Bin 0 -> 17464 bytes autogen.svg | 426 +++++ config.pdf | Bin 0 -> 14672 bytes config.svg | 223 +++ redcap.pdf | Bin 0 -> 13903 bytes redcap.svg | 148 ++ sfrc01042-gridss.pdf | Bin 0 -> 24223 bytes sfrc01042-gridss.svg | 3784 +++++++++++++++++++++++++++++++++++++ sfrc01042.pdf | Bin 0 -> 79461 bytes sfrc01042.svg | 5065 ++++++++++++++++++++++++++++++++++++++++++++++++++ slides.tex | 101 +- 11 files changed, 9726 insertions(+), 21 deletions(-) create mode 100644 autogen.pdf create mode 100644 autogen.svg create mode 100644 config.pdf create mode 100644 config.svg create mode 100644 redcap.pdf create mode 100644 redcap.svg create mode 100644 sfrc01042-gridss.pdf create mode 100644 sfrc01042-gridss.svg create mode 100644 sfrc01042.pdf create mode 100644 sfrc01042.svg diff --git a/autogen.pdf b/autogen.pdf new file mode 100644 index 0000000..fa9bb2d Binary files /dev/null and b/autogen.pdf differ diff --git a/autogen.svg b/autogen.svg new file mode 100644 index 0000000..0db0c5a --- /dev/null +++ b/autogen.svg @@ -0,0 +1,426 @@ + + + + + + + + + + + + + + image/svg+xml + + + + + + + with import ./milton-slurm.nix { }; +let + samples = [ + { + site = "B1"; + class = "normals"; + pdx = false; + r1 = + "mz/Vf/SHA256E-s23731819040--c650db8ef7fcd00178178fd254970d989b1a964ee68b887f56ae0586683f7c0a.gz/SHA256E-s23731819040--c650db8ef7fcd00178178fd254970d989b1a964ee68b887f56ae0586683f7c0a.gz"; + r2 = + "kz/Zq/SHA256E-s25775609303--bfe116906bddf9799ba78d78be56938b21910812bebcf947f0c56cfbd5fc650a.gz/SHA256E-s25775609303--bfe116906bddf9799ba78d78be56938b21910812bebcf947f0c56cfbd5fc650a.gz"; + } + { + site = "B1"; + class = "normals"; + pdx = false; + r1 = + "V4/Wj/SHA256E-s17295801172--19e79e9018a60ea5715481973ff92194f6a218e5f04418303d99a2eafbaac7d9.gz/SHA256E-s17295801172--19e79e9018a60ea5715481973ff92194f6a218e5f04418303d99a2eafbaac7d9.gz"; + r2 = + "j7/z8/SHA256E-s18960756093--07bdcea8a80adfbf021c9082b1de5dd9a27d7325ecbff0122b82d8654245ed20.gz/SHA256E-s18960756093--07bdcea8a80adfbf021c9082b1de5dd9a27d7325ecbff0122b82d8654245ed20.gz"; + } + { + site = "S1"; + class = "tumours"; + pdx = false; + r1 = + "Fm/94/SHA256E-s4503271082--528808192a494d4e8dc98c0596ee8d04e45cd65c70957993ffdf6a8c2294dd51.gz/SHA256E-s4503271082--528808192a494d4e8dc98c0596ee8d04e45cd65c70957993ffdf6a8c2294dd51.gz"; + r2 = + "q2/Zk/SHA256E-s4582653633--d32ee809bd7d19ed497938a7a5ee36117b8f3f1b43109482da174555bcb1a45e.gz/SHA256E-s4582653633--d32ee809bd7d19ed497938a7a5ee36117b8f3f1b43109482da174555bcb1a45e.gz"; + } + { + site = "S1"; + class = "tumours"; + pdx = false; + r1 = + "Kf/w5/SHA256E-s34952768707--cc01c16aea8cdf162e439c8c7cb419bcb381efe95c071b9e6b97771b40f1eff8.gz/SHA256E-s34952768707--cc01c16aea8cdf162e439c8c7cb419bcb381efe95c071b9e6b97771b40f1eff8.gz"; + r2 = + "Gg/gk/SHA256E-s37880355076--e10fc22839c91f8900ef98afd473361ef0dcb1882b92f87140a9000237fac0e6.gz/SHA256E-s37880355076--e10fc22839c91f8900ef98afd473361ef0dcb1882b92f87140a9000237fac0e6.gz"; + } + { + site = "S1"; + class = "tumours"; + pdx = false; + r1 = + "xM/Q9/SHA256E-s38656117968--04dc46ef77fef4a5578d00d073682d433dfeb6337b905a2cc822b685e0cf61ea.gz/SHA256E-s38656117968--04dc46ef77fef4a5578d00d073682d433dfeb6337b905a2cc822b685e0cf61ea.gz"; + r2 = + "Jq/6j/SHA256E-s42454148279--ec5c092b13b76197e2659c51f11bf17c78b2caa44789c4fe006844f8bd15561e.gz/SHA256E-s42454148279--ec5c092b13b76197e2659c51f11bf17c78b2caa44789c4fe006844f8bd15561e.gz"; + } + ]; +in import ./multisample.nix { + inherit bionix samples fetch; + name = "SFRC01247"; +} + + + SBJ00237,MDX190227,L1901038,SFRC01247,SFRC01247-B1 +SBJ00237,MDX190227,L1901038_topup,SFRC01247,SFRC01247-B1 +SBJ00237,MDX190228,L1901026,SFRC01247,SFRC01247-S1 +SBJ00237,MDX190228,L1901039,SFRC01247,SFRC01247-S1 +SBJ00237,MDX190228,L1901039_topup,SFRC01247,SFRC01247-S1 +SBJ00239,MDX190220,L1901031,SFRC01222,SFRC01222-S1 +SBJ00239,MDX190220,L1901031_topup,SFRC01222,SFRC01222-S1 +SBJ00239,MDX190221,L1901032,SFRC01222,SFRC01222-B1 +SBJ00239,MDX190221,L1901032_topup,SFRC01222,SFRC01222-B1 +SBJ00240,MDX190222,L1901033,SFRC01228,SFRC01228-S1 +SBJ00240,MDX190222,L1901033_topup,SFRC01228,SFRC01228-S1 +SBJ00240,MDX190223,L1901034,SFRC01228,SFRC01228-B1 +SBJ00240,MDX190223,L1901034_topup,SFRC01228,SFRC01228-B1 +SBJ00268,PRJ200049,L2000061,SFRC01233,SFRC01233-S1 +SBJ00268,PRJ200050,L2000062,SFRC01233,SFRC01233-B1 +SBJ00284,PRJ200066,L2000102,SFRC01120,SFRC01120-A-E1 +SBJ00284,PRJ200067,L2000103,SFRC01120,SFRC01120-B1 +SBJ00304,PRJ200056,L2000153,SFRC01260,SFRC01260-B1 +SBJ00304,PRJ200202,L2000152,SFRC01260,SFRC01260-S1 +SBJ00307,PRJ200211,L2000166,SFRC01172,SFRC01172-B1 +SBJ00307,PRJ200212,L2000167,SFRC01172,SFRC01172-S1S3 +SBJ00308,PRJ200213,L2000168,SFRC1265,SFRC1265-B1 +SBJ00308,PRJ200214,L2000169,SFRC1265,SFRC1265-S1 +SBJ00346,PRJ200267,L2000235,SFRC01273,PRJ200267-SFRC01273-B1 +SBJ00346,PRJ200268,L2000236,SFRC01273,PRJ200268-SFRC01273-S1 +SBJ00349,PRJ200304,L2000264,SFRC01232,SFRC01232-B1 +SBJ00349,PRJ200305,L2000265,SFRC01232,SFRC01232-S2 + + + + diff --git a/config.pdf b/config.pdf new file mode 100644 index 0000000..438cd47 Binary files /dev/null and b/config.pdf differ diff --git a/config.svg b/config.svg new file mode 100644 index 0000000..5579b6e --- /dev/null +++ b/config.svg @@ -0,0 +1,223 @@ + + + + + + + + + + + + + + image/svg+xml + + + + + + + { bionix, speed ? "normal", max-genotypes ? 0, targets ? [] }: + + + { + options.octopus.call = { + speed = mkOption { + type = types.enum [ "normal" "fast" "very-fast" ]; + default = "normal"; + }; + + max-genotypes = mkOption { + type = types.int; + default = 0; + description = "Maximum number of candidate genotypes. If zero then flag is not passed to octopus." + }; + + targets = mkOption { + type = types.either (types.listOf types.str) types.path; + default = []; + description = "either a list of genomic regions to call or a file containing a list of genomic regions to call"; + example = '' + targets = [ "chr1" "chr2:0-1,000" ]; + ''; + }; + }; +... + + diff --git a/redcap.pdf b/redcap.pdf new file mode 100644 index 0000000..a3be593 Binary files /dev/null and b/redcap.pdf differ diff --git a/redcap.svg b/redcap.svg new file mode 100644 index 0000000..f1a4da7 --- /dev/null +++ b/redcap.svg @@ -0,0 +1,148 @@ + + + + + + + + image/svg+xml + + + + + + + with import ./milton-slurm.nix { };with bionix;let samples = [...];in import ./multisample.nix { redcap = { meeting_discussions_follow_up = '' ...''; case_details = ...; tumour_details = ...; date_of_death = ...; }; inherit bionix samples fetch; name = "SFRC01270";} + + diff --git a/sfrc01042-gridss.pdf b/sfrc01042-gridss.pdf new file mode 100644 index 0000000..158ac91 Binary files /dev/null and b/sfrc01042-gridss.pdf differ diff --git a/sfrc01042-gridss.svg b/sfrc01042-gridss.svg new file mode 100644 index 0000000..8202d01 --- /dev/null +++ b/sfrc01042-gridss.svg @@ -0,0 +1,3784 @@ + + + + + + + + image/svg+xml + + + + + + + + cmi8n2kwcyf5zjf4jcjrk1qan7c7qk54-bionix-samtools-sort.drv + + bionix-samtools-sort.drv + + + cqcqfwy7hg64z88ali8i51yqh4iqv5wh-bionix-gridss-annotateVariants.drv + + bionix-gridss-annotateVariants.drv + + + cmi8n2kwcyf5zjf4jcjrk1qan7c7qk54-bionix-samtools-sort.drv->cqcqfwy7hg64z88ali8i51yqh4iqv5wh-bionix-gridss-annotateVariants.drv + + + + + 7m2md5fnmcdsg3zaplz78aqi7wxrk60g-bionix-gridss-identifyVariants.drv + + bionix-gridss-identifyVariants.drv + + + cmi8n2kwcyf5zjf4jcjrk1qan7c7qk54-bionix-samtools-sort.drv->7m2md5fnmcdsg3zaplz78aqi7wxrk60g-bionix-gridss-identifyVariants.drv + + + + + iss5z12ifpydd2lnxzvxl70nqlg3imwm-bionix-samtools-index.drv + + bionix-samtools-index.drv + + + cmi8n2kwcyf5zjf4jcjrk1qan7c7qk54-bionix-samtools-sort.drv->iss5z12ifpydd2lnxzvxl70nqlg3imwm-bionix-samtools-index.drv + + + + + k038yp2ns7gr62zcas06gr4qwlvz1ja9-bionix-gridss-collectMetrics.drv + + bionix-gridss-collectMetrics.drv + + + cmi8n2kwcyf5zjf4jcjrk1qan7c7qk54-bionix-samtools-sort.drv->k038yp2ns7gr62zcas06gr4qwlvz1ja9-bionix-gridss-collectMetrics.drv + + + + + vzq8qp1jkb90nn3srx7qmj8rfm65zb5g-bionix-gridss-extractSVReads.drv + + bionix-gridss-extractSVReads.drv + + + jl1hqccsrxmr2gz8sw6kfj7y71yigrlg-bionix-gridss-collectMetrics.drv + + bionix-gridss-collectMetrics.drv + + + s92xv75j52snxjpyld2f2pd9lylnqqrn-bionix-gridss-extractSVReads.drv + + bionix-gridss-extractSVReads.drv + + + grsy3dpm1hzzlaxfz5qs8i0i1awsw87p-bionix-gridss-collectMetrics.drv + + bionix-gridss-collectMetrics.drv + + + zyp4qhcfrcp3hncccy4qm2zc0dx9c7xp-bionix-gridss-extractSVReads.drv + + bionix-gridss-extractSVReads.drv + + + fi9mw3jshd5mhd2i2n12x91c9nplwqpq-bionix-gridss-collectMetrics.drv + + bionix-gridss-collectMetrics.drv + + + bh9np1j6vxal6ahjsp4jrbjp7kgwl6az-bionix-gridss-softClipsToSplitReads.drv + + bionix-gridss-softClipsToSplitReads.drv + + + 42y10r3hb6nh803vfaq04ak7k4jyqxvv-bionix-gridss-assemble.drv + + bionix-gridss-assemble.drv + + + brabadaz6f8zfrjgkx228svfw4hnj6jh-bionix-gridss-assemble.drv + + bionix-gridss-assemble.drv + + + c0yc7d0as8qgkhnirpw4n86zw3jn3zvj-bionix-gridss-assemble.drv + + bionix-gridss-assemble.drv + + + caisv3z5hf72vrayb5j0zp07v8kyanas-bionix-gridss-assemble.drv + + bionix-gridss-assemble.drv + +