New parameter example for iris

joechanlab · Jul 22, 2024 · f87cb86 · f87cb86
1 parent ae71253
commit f87cb86
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/params.yml b/params.yml
@@ -1,5 +1,5 @@
 samplesheet: "./data/sampleSheet.csv"
-outdir: "../scratch/"
+outdir: "./data/results/"
 experiment:
     name: "toy_data"
 cellbender:
@@ -11,6 +11,9 @@ postprocessing:
     n_pca_components: 3
     n_diffmap_components: 3
     metadata: "None"
+celltypist:
+    model: "Immune_All_Low.pkl"
+mount: "/data1,/home,/scratch"
 with_gpu: true
 max_memory: "6.GB"
 max_cpus: 6

diff --git a/run_test.sh b/run_test.sh
@@ -1,9 +1,10 @@
 module load singularity/3.7.1
-module load gcc/10.2.0
-module load cuda/11.7
-export NXF_SINGULARITY_CACHEDIR="/lila/data/chanjlab/wangm10/work-nf-scrnaseq/singularity/"
+module load gcc/12.2.0
+module load cuda/12.0
+#export NXF_SINGULARITY_CACHEDIR="/lila/data/chanjlab/wangm10/work-nf-scrnaseq/singularity/"
+export NXF_SINGULARITY_CACHEDIR="/usersoftware/chanj3/singularity/"
 
-nextflow run ./main.nf -resume -profile lilac -params-file ./params.yml -w "/lila/data/chanjlab/wangm10/scratch/"
+nextflow run ./main.nf -resume -profile iris -params-file ./params.yml -w "/scratch/chanj3/wangm10/work"
 # nextflow run ./main.nf -resume 0b2aab78-3380-47e5-bf3a-d2babb788b9f -profile lilac -params-file ./params.yml -w "../work-cellbender-test/"
 
 # nextflow run ./main.nf -resume -profile singularity -params-file ../oliver_RPMN_2024/oliver_RPMN_2024_params.yml -w "/lila/data/chanjlab/wangm10/work-nf-scrnaseq/"