update saige-qtl image with new step3 (#127)

* update saige-qtl image with new step3

* add test data files to image

* update commit hash to trigger new build

* input output files do not need to be executable

images.toml

@@ -20,7 +20,7 @@ peer = '1.3'
 picard = '2.27.4'
 reviewer = '0.2.7'
 reviewer_bw2 = '0.2.7-bw2-fork-0.2'
-saige-qtl = '1bdfe8408a17f7da8b0453a697a867f412f48bcc'
+saige-qtl = '41a4dcae69d83a2eb02fb4491a0148d25e4d46db'
 sambamba = '1.0.1'
 samblaster = '0.1.26'
 samtools = '1.18'

images/saige-qtl/Dockerfile

@@ -20,11 +20,17 @@ RUN apt-get update && \
     R CMD INSTALL . && \
     mv extdata/step1_fitNULLGLMM_qtl.R \
        extdata/step2_tests_qtl.R \
-       extdata/step3_LDmat.R \
-       extdata/createSparseGRM.R /usr/local/bin/ && \
+       extdata/step3_gene_pvalue_qtl.R \
+       extdata/input/n.indep_100_n.cell_1_01.step1 \
+       extdata/input/seed_1_100_nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_Poisson.txt \
+       extdata/input/genotype_10markers.vcf.gz \
+       extdata/input/genotype_10markers.vcf.gz.csi \
+       extdata/input/gene_1_cis_region.txt \
+       extdata/output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1 \
+       extdata/output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis \
+       extdata/output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis_genePval /usr/local/bin/ && \
     chmod a+x /usr/local/bin/step1_fitNULLGLMM_qtl.R \
               /usr/local/bin/step2_tests_qtl.R \
-              /usr/local/bin/step3_LDmat.R \
-              /usr/local/bin/createSparseGRM.R && \
+              /usr/local/bin/step3_gene_pvalue_qtl.R && \
     cd .. && \
     rm -r qtl