Merge pull request #1223 from milaboratory/mixcr-regression-tests/fin…

…al-440-fixes Regression tests changes in the final-440-fixes
milaboratory · Jul 3, 2023 · abe4b00 · abe4b00
2 parents 4b5e5d1 + 3b223f7
commit abe4b00
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Showing 183 changed files with 752 additions and 167 deletions.
diff --git a/regression/cli-help/align.txt b/regression/cli-help/align.txt
@@ -6,8 +6,8 @@ Usage: mixcr align --preset <preset> [--strict-sample-sheet-matching] [--trimmin
                    [--not-aligned-R2 <path.fastq[.gz]>] [--not-parsed-I1 <path.fastq[.gz]>]
                    [--not-parsed-I2 <path.fastq[.gz]>] [--not-parsed-R1 <path.fastq[.gz]>]
                    [--not-parsed-R2 <path.fastq[.gz]>] [--species <species>] [--library <library>]
-                   [--split-by-sample] [--dont-split-by-sample] [--sample-table sample_table.tsv]
-                   [--sample-table-strict sample_table.tsv] [--dna] [--rna]
+                   [--split-by-sample] [--dont-split-by-sample] [--sample-sheet sample_sheet.tsv]
+                   [--sample-sheet-strict sample_sheet.tsv] [--dna] [--rna]
                    [--floating-left-alignment-boundary [<anchor_point>]]
                    [--rigid-left-alignment-boundary [<anchor_point>]]
                    [--floating-right-alignment-boundary (<gene_type>|<anchor_point>)]
@@ -97,10 +97,10 @@ Builds alignments with V,D,J and C genes for input sequencing reads.
                                library is used. One can also use external libraries
       --split-by-sample      Split output alignments files by sample.
       --dont-split-by-sample Don't split output alignments files by sample.
-      --sample-table sample_table.tsv
+      --sample-sheet sample_sheet.tsv
                              Loads sample table from a tab separated file (one substitution will be
                                allowed during matching)
-      --sample-table-strict sample_table.tsv
+      --sample-sheet-strict sample_sheet.tsv
                              Loads sample table from a tab separated file (strict matching will be
                                used).
       --dna                  For DNA starting material. Setups V gene feature to align to

diff --git a/regression/cli-help/analyze.txt b/regression/cli-help/analyze.txt
@@ -1,6 +1,6 @@
 Usage: mixcr analyze [--add-step <step>] [--remove-step <step>] [-s <species>] [-b <library>]
-                     [--split-by-sample] [--dont-split-by-sample] [--sample-table sample_table.tsv]
-                     [--sample-table-strict sample_table.tsv] [--dna] [--rna]
+                     [--split-by-sample] [--dont-split-by-sample] [--sample-sheet sample_sheet.tsv]
+                     [--sample-sheet-strict sample_sheet.tsv] [--dna] [--rna]
                      [--floating-left-alignment-boundary [<anchor_point>]]
                      [--rigid-left-alignment-boundary [<anchor_point>]]
                      [--floating-right-alignment-boundary (<gene_type>|<anchor_point>)]
@@ -61,10 +61,10 @@ Params for align command:
                                library is used. One can also use external libraries
       --split-by-sample      Split output alignments files by sample.
       --dont-split-by-sample Don't split output alignments files by sample.
-      --sample-table sample_table.tsv
+      --sample-sheet sample_sheet.tsv
                              Loads sample table from a tab separated file (one substitution will be
                                allowed during matching)
-      --sample-table-strict sample_table.tsv
+      --sample-sheet-strict sample_sheet.tsv
                              Loads sample table from a tab separated file (strict matching will be
                                used).
       --dna                  For DNA starting material. Setups V gene feature to align to

diff --git a/regression/cli-help/exportPreset.txt b/regression/cli-help/exportPreset.txt
@@ -1,6 +1,6 @@
 Usage: mixcr exportPreset [--no-validation] [--add-step <step>] [--remove-step <step>] [-s
                           <species>] [-b <library>] [--split-by-sample] [--dont-split-by-sample]
-                          [--sample-table sample_table.tsv] [--sample-table-strict sample_table.
+                          [--sample-sheet sample_sheet.tsv] [--sample-sheet-strict sample_sheet.
                           tsv] [--dna] [--rna] [--floating-left-alignment-boundary
                           [<anchor_point>]] [--rigid-left-alignment-boundary [<anchor_point>]]
                           [--floating-right-alignment-boundary (<gene_type>|<anchor_point>)]
@@ -44,10 +44,10 @@ Params for align command:
                                library is used. One can also use external libraries
       --split-by-sample      Split output alignments files by sample.
       --dont-split-by-sample Don't split output alignments files by sample.
-      --sample-table sample_table.tsv
+      --sample-sheet sample_sheet.tsv
                              Loads sample table from a tab separated file (one substitution will be
                                allowed during matching)
-      --sample-table-strict sample_table.tsv
+      --sample-sheet-strict sample_sheet.tsv
                              Loads sample table from a tab separated file (strict matching will be
                                used).
       --dna                  For DNA starting material. Setups V gene feature to align to

diff --git a/regression/presets/analyze/10x-5gex-cdr3.yaml b/regression/presets/analyze/10x-5gex-cdr3.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-5gex-full-length.yaml b/regression/presets/analyze/10x-5gex-full-length.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-5gex.yaml b/regression/presets/analyze/10x-5gex.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj-bcr-full-length.yaml b/regression/presets/analyze/10x-vdj-bcr-full-length.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj-bcr.yaml b/regression/presets/analyze/10x-vdj-bcr.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-alias-multi-barcode-test.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj-tcr-full-length.yaml b/regression/presets/analyze/10x-vdj-tcr-full-length.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml b/regression/presets/analyze/10x-vdj-tcr-multi-barcode-test.yaml
@@ -21,6 +21,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml b/regression/presets/analyze/10x-vdj-tcr-qc-test.yaml
@@ -8,9 +8,6 @@ pipeline:
 - assemble
 - assembleContigs
 - exportClones
-validation:
-- type: TagPatternShouldContainsTagType
-  tagType: Cell
 align:
   species: ""
   libraryName: default
@@ -26,6 +23,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustContainTagType
+    tagType: Cell
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj-tcr.yaml b/regression/presets/analyze/10x-vdj-tcr.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/10x-vdj.yaml b/regression/presets/analyze/10x-vdj.yaml
@@ -23,6 +23,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-bcr-cdr3.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/abhelix-human-bcr-full-length.yaml b/regression/presets/analyze/abhelix-human-bcr-full-length.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml b/regression/presets/analyze/abhelix-human-tcr-cdr3.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/abhelix-human-tcr-full-length.yaml b/regression/presets/analyze/abhelix-human-tcr-full-length.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/abhelix-human.yaml b/regression/presets/analyze/abhelix-human.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-cdr3.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml b/regression/presets/analyze/ampliseq-tcrb-plus-full-length.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/ampliseq-tcrb-plus.yaml b/regression/presets/analyze/ampliseq-tcrb-plus.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml b/regression/presets/analyze/ampliseq-tcrb-sr-cdr3.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/ampliseq-tcrb-sr.yaml b/regression/presets/analyze/ampliseq-tcrb-sr.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-full-length.yaml
@@ -22,6 +22,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v1.yaml
@@ -27,6 +27,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-bcr-v2.yaml
@@ -30,6 +30,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-full-length.yaml
@@ -22,6 +22,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v1.yaml
@@ -24,6 +24,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-human-tcr-v2.yaml
@@ -27,6 +27,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-full-length.yaml
@@ -22,6 +22,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v1.yaml
@@ -31,6 +31,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-bcr-v2.yaml
@@ -34,6 +34,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-full-length.yaml
@@ -22,6 +22,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v1.yaml
@@ -25,6 +25,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml b/regression/presets/analyze/bd-rhapsody-mouse-tcr-v2.yaml
@@ -28,6 +28,7 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations: []
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml b/regression/presets/analyze/biomed2-human-bcr-cdr3.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/biomed2-human-bcr-full-length.yaml b/regression/presets/analyze/biomed2-human-bcr-full-length.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters:

diff --git a/regression/presets/analyze/biomed2-human-igh.yaml b/regression/presets/analyze/biomed2-human-igh.yaml
@@ -18,6 +18,9 @@ align:
   tagMaxBudget: 10.0
   readIdAsCellTag: false
   sampleTable: null
+  tagsValidations:
+  - type: MustNotContainTagType
+    tagType: Sample
   splitBySample: false
   limit: null
   parameters: