From fe6c52d3e1035baeb18b6acad4ed05bbaa173f40 Mon Sep 17 00:00:00 2001 From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Date: Mon, 17 Jul 2023 09:59:49 +0200 Subject: [PATCH 01/91] =?UTF-8?q?Ajout=C3=A9(e)=20Diagramme=20sans=20nom.d?= =?UTF-8?q?rawio?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/Diagramme sans nom.drawio | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 docs/Diagramme sans nom.drawio diff --git a/docs/Diagramme sans nom.drawio b/docs/Diagramme sans nom.drawio new file mode 100644 index 00000000..a18dcc8a --- /dev/null +++ b/docs/Diagramme sans nom.drawio @@ -0,0 +1,10 @@ + + + + + + + + + + From 9f067d8b4822a438c1ad8c55ab45bd89df98304c Mon Sep 17 00:00:00 2001 From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Date: Tue, 18 Jul 2023 09:19:56 +0200 Subject: [PATCH 02/91] =?UTF-8?q?Ajout=C3=A9(e)=20metro=5Fmap.drawio.svg?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/metro_map.drawio.svg | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 docs/metro_map.drawio.svg diff --git a/docs/metro_map.drawio.svg b/docs/metro_map.drawio.svg new file mode 100644 index 00000000..9b26edf5 --- /dev/null +++ b/docs/metro_map.drawio.svg @@ -0,0 +1,4 @@ + + + + \ No newline at end of file From 17238be3420d842f704fb8b1b771645609e20f25 Mon Sep 17 00:00:00 2001 From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Date: Tue, 18 Jul 2023 13:56:56 +0200 Subject: [PATCH 03/91] Added NFCore_library.xml --- docs/NFCore_library.xml | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/NFCore_library.xml diff --git a/docs/NFCore_library.xml b/docs/NFCore_library.xml new file mode 100644 index 00000000..44c291f5 --- /dev/null +++ b/docs/NFCore_library.xml @@ -0,0 +1 @@ +[] \ No newline at end of file From 1049142c110b05857844d07f6f37ef7643292a1b Mon Sep 17 00:00:00 2001 From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Date: Tue, 18 Jul 2023 13:59:03 +0200 Subject: [PATCH 04/91] Added Nf-Core.xml --- docs/Nf-Core.xml | 120 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 120 insertions(+) create mode 100644 docs/Nf-Core.xml diff --git a/docs/Nf-Core.xml b/docs/Nf-Core.xml new file mode 100644 index 00000000..6d1cadde --- /dev/null +++ b/docs/Nf-Core.xml @@ -0,0 +1,120 @@ +[ + { + "xml": "<mxGraphModel><root><mxCell id=\"0\"/><mxCell id=\"1\" parent=\"0\"/><mxCell id=\"2\" value=\"\" style=\"group\" vertex=\"1\" connectable=\"0\" parent=\"1\"><mxGeometry y=\"15\" width=\"20\" height=\"45\" as=\"geometry\"/></mxCell><mxCell id=\"3\" value=\"\" style=\"ellipse;whiteSpace=wrap;html=1;aspect=fixed;rounded=1;rotation=0;strokeWidth=2;\" vertex=\"1\" parent=\"2\"><mxGeometry width=\"20\" height=\"20\" relative=\"1\" as=\"geometry\"><mxPoint y=\"-15\" as=\"offset\"/></mxGeometry></mxCell><mxCell id=\"4\" value=\"\" 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deletion(-) diff --git a/docs/metro_map.drawio.svg b/docs/metro_map.drawio.svg index 9b26edf5..1c0974cd 100644 --- a/docs/metro_map.drawio.svg +++ b/docs/metro_map.drawio.svg @@ -1,4 +1,4 @@ - \ No newline at end of file +FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 2ImputationImputationBeagleBeagleSequenceSequenceGenotypeGenotypeBeagleBeagleShapeit 5 / Minimap 5Shapeit 5...PhasingPhasingShapeit 5Shapeit 5FastqFastqFastqFastqReference panel VCFReference panel...BAM High coverageBAM High covera...SimulationSimulationType ?Type ?PreprocessingPreprocessingVCF imputedVCF imputedFastqFastqFastqFastqReference .binReference .binValidationValidationFastqFastqFastqFastqPhased reference panel VCFPhased referenc...FASTAFASTABAMBAMVCFVCFVCF callingVCF callingText is not SVG - cannot display \ No newline at end of file From f6684da3dec0c7d7d41e51c5916a758e753f77d6 Mon Sep 17 00:00:00 2001 From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Date: Tue, 18 Jul 2023 15:11:35 +0200 Subject: [PATCH 07/91] Update metro_map.drawio.svg --- docs/metro_map.drawio.svg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/metro_map.drawio.svg b/docs/metro_map.drawio.svg index 1c0974cd..d54316ef 100644 --- a/docs/metro_map.drawio.svg +++ b/docs/metro_map.drawio.svg @@ -1,4 +1,4 @@ -FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 2ImputationImputationBeagleBeagleSequenceSequenceGenotypeGenotypeBeagleBeagleShapeit 5 / Minimap 5Shapeit 5...PhasingPhasingShapeit 5Shapeit 5FastqFastqFastqFastqReference panel VCFReference panel...BAM High coverageBAM High covera...SimulationSimulationType ?Type ?PreprocessingPreprocessingVCF imputedVCF imputedFastqFastqFastqFastqReference .binReference .binValidationValidationFastqFastqFastqFastqPhased reference panel VCFPhased referenc...FASTAFASTABAMBAMVCFVCFVCF callingVCF callingText is not SVG - cannot display \ No newline at end of file +FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 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b/docs/metro_map.drawio.svg index d54316ef..940e65e2 100644 --- a/docs/metro_map.drawio.svg +++ b/docs/metro_map.drawio.svg @@ -1,4 +1,4 @@ -FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 2ImputationImputationBeagleBeagleSequenceSequenceGenotypeGenotypeBeagleBeagleShapeit 5 / Minimap 5Shapeit 5...PhasingPhasingShapeit 5Shapeit 5FastqFastqFastqFastqReference panel VCFReference panel...BAM High coverageBAM High covera...SimulationSimulationType ?Type ?PreprocessingPreprocessingVCF imputedVCF imputedFastqFastqFastqFastqReference .binReference .binValidationValidationFastqFastqFastqFastqPhased reference panel VCFPhased referenc...FASTAFASTABAMBAMVCFVCFVCF callingVCF callingSciKit alleleSciKit alleleDownsampleDownsampleCSVImputed correlationCSV...Text is not SVG - cannot display \ No newline at end of file +FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 2ImputationImputationBeagleBeagleSequenceSequenceGenotypeGenotypeBeagleBeagleShapeit 5 / Minimap 5Shapeit 5...PhasingPhasingShapeit 5Shapeit 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100644 --- a/docs/metro_map.drawio.svg +++ b/docs/metro_map.drawio.svg @@ -1,4 +1,4 @@ -FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 2ImputationImputationBeagleBeagleSequenceSequenceGenotypeGenotypeBeagleBeagleShapeit 5 / Minimap 5Shapeit 5...PhasingPhasingShapeit 5Shapeit 5FastqFastqFastqFastqReference panel VCFReference panel...BAM High coverageBAM High covera...SimulationSimulationType ?Type ?PreprocessingPreprocessingVCF imputedVCF imputedFastqFastqFastqFastqReference .binReference .binFastqFastqFastqFastqPhased reference panel VCFPhased referenc...FASTAFASTABAMBAMVCFVCFVCF callingVCF callingSciKit alleleSciKit alleleDownsampleDownsampleCSVImputed correlationCSV...List of position (SNP chip array)List of positio...SNP selectionSNP select...ValidationValidationAlignmentAlignmentCallingCallingText is not SVG - cannot display \ No newline at end of file +FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 2ImputationImputationBeagleBeagleSequenceSequenceGenotypeGenotypeBeagleBeagleShapeit 5 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a/docs/metro_map.drawio.svg b/docs/metro_map.drawio.svg index de981692..424a8185 100644 --- a/docs/metro_map.drawio.svg +++ b/docs/metro_map.drawio.svg @@ -1,4 +1,4 @@ -FastqFastqGlimpse 1Glimpse 1Glimpse 2Glimpse 2ImputationImputationBeagleBeagleSequenceSequenceGenotypeGenotypeBeagleBeagleShapeit 5 / Minimap 5Shapeit 5...PhasingPhasingShapeit 5Shapeit 5FastqFastqFastqFastqReference panel VCFReference panel...BAM High coverageBAM High covera...SimulationSimulationType ?Type ?PreprocessingPreprocessingVCF imputedVCF imputedFastqFastqFastqFastqReference .binReference .binFastqFastqFastqFastqPhased reference panel VCFPhased referenc...FASTAFASTABAMBAMVCFVCFVCF callingVCF callingSciKit alleleSciKit alleleDownsampleDownsampleCSVImputed correlationCSV...List of position (SNP chip array)List of positio...SNP selectionSNP select...ValidationValidationAlignmentAlignmentCallingCallingPositionsPositionsText is not SVG - cannot display \ No newline at end of file +FastqFastqGlimpse 1Glimpse 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14:08:47 +0200 Subject: [PATCH 11/91] Delete not used library --- docs/Diagramme sans nom.drawio | 10 -- docs/Nf-Core.xml | 120 ----------------- docs/NfCore_library.xml | 238 ++++++++++++++++----------------- 3 files changed, 119 insertions(+), 249 deletions(-) delete mode 100644 docs/Diagramme sans nom.drawio delete mode 100644 docs/Nf-Core.xml diff --git a/docs/Diagramme sans nom.drawio b/docs/Diagramme sans nom.drawio deleted file mode 100644 index a18dcc8a..00000000 --- a/docs/Diagramme sans nom.drawio +++ /dev/null @@ -1,10 +0,0 @@ - - - - - - - - - - diff --git a/docs/Nf-Core.xml b/docs/Nf-Core.xml deleted file mode 100644 index 6d1cadde..00000000 --- a/docs/Nf-Core.xml +++ /dev/null @@ -1,120 +0,0 @@ -[ - { - "xml": "<mxGraphModel><root><mxCell id=\"0\"/><mxCell id=\"1\" parent=\"0\"/><mxCell id=\"2\" value=\"\" style=\"group\" vertex=\"1\" connectable=\"0\" parent=\"1\"><mxGeometry y=\"15\" width=\"20\" height=\"45\" as=\"geometry\"/></mxCell><mxCell id=\"3\" value=\"\" 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style=\"endArrow=none;html=1;rounded=1;strokeWidth=2;\" edge=\"1\" parent=\"1\"><mxGeometry width=\"50\" height=\"50\" relative=\"1\" as=\"geometry\"><mxPoint as=\"sourcePoint\"/><mxPoint x=\"40\" y=\"20\" as=\"targetPoint\"/><Array as=\"points\"><mxPoint x=\"20\"/></Array></mxGeometry></mxCell></root></mxGraphModel>", + "w": 40, + "h": 20, + "aspect": "fixed", + "title": "line_45" + }, + { + "xml": "<mxGraphModel><root><mxCell id=\"0\"/><mxCell id=\"1\" parent=\"0\"/><mxCell id=\"2\" value=\"\" style=\"endArrow=none;html=1;rounded=1;strokeWidth=2;\" edge=\"1\" parent=\"1\"><mxGeometry width=\"50\" height=\"50\" relative=\"1\" as=\"geometry\"><mxPoint as=\"sourcePoint\"/><mxPoint x=\"40\" y=\"40\" as=\"targetPoint\"/><Array as=\"points\"><mxPoint x=\"20\"/><mxPoint x=\"40\" y=\"20\"/></Array></mxGeometry></mxCell></root></mxGraphModel>", + "w": 40, + "h": 40, + "aspect": "fixed" + } ] \ No newline at end of file From f4d1ddc8c11a835d96f123d3396ca56c5e5919f4 Mon Sep 17 00:00:00 2001 From: LouisBzh Date: Thu, 20 Jul 2023 14:10:03 +0200 Subject: [PATCH 12/91] Delete old library --- docs/NFCore_library.xml | 1 - ...re_library.xml => NfCore_library copy.xml} | 238 +++++++++--------- 2 files changed, 119 insertions(+), 120 deletions(-) delete mode 100644 docs/NFCore_library.xml rename docs/{NfCore_library.xml => NfCore_library copy.xml} (99%) diff --git a/docs/NFCore_library.xml b/docs/NFCore_library.xml deleted file mode 100644 index 44c291f5..00000000 --- a/docs/NFCore_library.xml +++ /dev/null @@ -1 +0,0 @@ -[] \ No newline at end of file diff --git a/docs/NfCore_library.xml b/docs/NfCore_library copy.xml similarity index 99% rename from docs/NfCore_library.xml rename to docs/NfCore_library copy.xml index 0f49ca71..6d1cadde 100644 --- a/docs/NfCore_library.xml +++ b/docs/NfCore_library copy.xml @@ -1,120 +1,120 @@ -[ - { - "xml": "<mxGraphModel><root><mxCell id=\"0\"/><mxCell id=\"1\" parent=\"0\"/><mxCell id=\"2\" value=\"\" style=\"group\" vertex=\"1\" 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=> NfCore_library.xml} (100%) diff --git a/docs/NfCore_library copy.xml b/docs/NfCore_library.xml similarity index 100% rename from docs/NfCore_library copy.xml rename to docs/NfCore_library.xml From 6da28a31904c5cc3eca7df9fa366ca35c407ebdc Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 20 Jul 2023 18:11:17 -0300 Subject: [PATCH 14/91] add diagram_imputation.drawio --- docs/diagram_imputation.drawio | 588 +++++++++++++++++++++++++++++++++ 1 file changed, 588 insertions(+) create mode 100644 docs/diagram_imputation.drawio diff --git a/docs/diagram_imputation.drawio b/docs/diagram_imputation.drawio new file mode 100644 index 00000000..fd873d67 --- /dev/null +++ b/docs/diagram_imputation.drawio @@ -0,0 +1,588 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 20 Jul 2023 18:12:13 -0300 Subject: [PATCH 15/91] add diagram_imputation.drawio --- docs/diagram_imputation.drawio | 354 ++++++++++++++++----------------- 1 file changed, 177 insertions(+), 177 deletions(-) diff --git a/docs/diagram_imputation.drawio b/docs/diagram_imputation.drawio index fd873d67..0b1734d7 100644 --- a/docs/diagram_imputation.drawio +++ b/docs/diagram_imputation.drawio @@ -1,121 +1,121 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -123,16 +123,16 @@ - + - + - + - + @@ -140,49 +140,49 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -191,49 +191,49 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -242,95 +242,95 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -339,247 +339,247 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + From f4a78fee9227994508dfc11ffbd3cec2995effe7 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 20 Jul 2023 18:13:56 -0300 Subject: [PATCH 16/91] add diagram_imputation.drawio.svg --- docs/diagram_imputation.drawio.svg | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 docs/diagram_imputation.drawio.svg diff --git a/docs/diagram_imputation.drawio.svg b/docs/diagram_imputation.drawio.svg new file mode 100644 index 00000000..b02bbc37 --- /dev/null +++ b/docs/diagram_imputation.drawio.svg @@ -0,0 +1,4 @@ + + + +.VCFReferencePanel.VCF...Reference panel preparation (one time only)Reference 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preprocessing_referenceReference panel positions VCFReference panel...Reference panel positions TSVReference panel...--mode imputation --tool (GLIMPSE1, GLIMPSE2, STITCH, etc)--mode imputation --tool (GLIMPSE1, GLIMPSE2, STITCH, etc)Chunks TXTChunks TXTChunks TXTChunks TXTChunks TXTChunks TXT--mode performance--mode performance groundtruthground...VCF imputedVCF imputedVCF imputedVCF imputedVCF imputedVCF imputedBCFTOOLS concatBCFTOOLS c...BCFTOOLS concatBCFTOOLS c...VCF imputedVCF imputedcorrelationplotscorrelation...Chunks TXTChunks TXTText is not SVG - cannot display \ No newline at end of file From 90cf0c4b1e822f4716468e013cc927967452bc49 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 16 Aug 2023 14:51:56 -0300 Subject: [PATCH 17/91] update diagram_imputation.drawio --- docs/diagram_imputation.drawio | 422 ++++++++++++++++++++++++++------- 1 file changed, 341 insertions(+), 81 deletions(-) diff --git a/docs/diagram_imputation.drawio b/docs/diagram_imputation.drawio index 0b1734d7..e6df1dd9 100644 --- a/docs/diagram_imputation.drawio +++ b/docs/diagram_imputation.drawio @@ -1,26 +1,29 @@ - + - + + + + - + - + - + - - + + @@ -29,19 +32,19 @@ - + - + - + - + - + @@ -73,41 +76,29 @@ - - - - - - - - - - - - - + - + - + - + - + - + @@ -206,16 +197,10 @@ - - - - - - - + @@ -233,15 +218,6 @@ - - - - - - - - - @@ -273,18 +249,10 @@ - - - - - - - - - + @@ -330,15 +298,6 @@ - - - - - - - - - @@ -378,11 +337,11 @@ - + - + @@ -391,7 +350,7 @@ - + @@ -414,7 +373,7 @@ - + @@ -445,16 +404,16 @@ - + - - + + - + @@ -475,7 +434,7 @@ - + @@ -502,19 +461,16 @@ - + - - - - + - + @@ -559,7 +515,7 @@ - + @@ -568,7 +524,7 @@ - + @@ -582,6 +538,310 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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