last set of fixes

PNNL-CompBio · Sep 15, 2023 · 220d5d0 · 220d5d0
1 parent a2a6b3a
commit 220d5d0
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Showing 5 changed files with 16 additions and 4 deletions.
diff --git a/metrics/correlations/deconv-corrXcelltypes-cwl-tool.cwl b/metrics/correlations/deconv-corrXcelltypes-cwl-tool.cwl
@@ -43,6 +43,7 @@ inputs:
     type: string
   sampleRep:
     type: int
+    default: 0
 
 outputs:
   corr:

diff --git a/metrics/data-sim/runSamplingManually.py b/metrics/data-sim/runSamplingManually.py
@@ -6,7 +6,7 @@
 import os
 
 filelist = []
-for i in [2,3,4]:
+for i in [3,4]:
 #    estring = 'cwltool simul-data-sampling.cwl --prot-sigs LM9 --simType prot --repNumber '+str(i)
 #    print(estring)
 #    os.system(estring)

diff --git a/metrics/figures/plot-figs.cwl b/metrics/figures/plot-figs.cwl
@@ -30,6 +30,7 @@ inputs:
         position: 4
    repNumber:
      type: int
+     default: 0
      inputBinding:
         position: 3
 

diff --git a/metrics/imm-subtypes/imm-args.yml b/metrics/imm-subtypes/imm-args.yml
@@ -1,11 +1,16 @@
 tissueTypes:
   - tumor
 cancerTypes:
-  - endometrial
+  - hnscc
+  - gbm
   - luad
-  - colon
+  - coad
   - ovarian
   - ccrcc
+  - lscc
+  - brca
+  - pdac
+  - ucec
 signatures:
   - LM7c
   - LM22

diff --git a/metrics/mrna-prot/pan-can-matrix.yml b/metrics/mrna-prot/pan-can-matrix.yml
@@ -1,9 +1,14 @@
 cancerTypes:
-  - endometrial
+  - ucec
+  - brca
+  - coad
+  - lscc
   - ccrcc
   - luad
   - hnscc
   - ovarian
+  - pdac
+  - gbm
 prot-algorithms:
   - mcpcounter
   - epic