try again one env after another

nf-core · Jan 11, 2024 · 46abe99 · 46abe99
1 parent 28e892d
commit 46abe99
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/.github/workflows/set_ncbench_config.sh b/.github/workflows/set_ncbench_config.sh
@@ -9,17 +9,18 @@
         # .base-quality-recalibration = "gatk4 v$GATK_VERSION" |
         # .realignment = "none" |
         # .variant-detection  = "strelka2 v$STRELKA_VERSION" |
+
+        #with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.subcategory;
+        #. = "NA12878-agilent" ) |
+        #with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.benchmark;
+        #. = "giab-NA12878-agilent-${READS}M" ) |
 for READS in 75 200; do
     yq --inplace "
         with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.labels;
         .site = "nf-core" |
         .pipeline = "nf-core/sarek v$PIPELINE_VERSION" |
         .genotyping = "none" |
         .reads = "${READS}M" ) |
-        with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.subcategory;
-        . = "NA12878-agilent" ) |
-        with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.benchmark;
-        . = "giab-NA12878-agilent-${READS}M" ) |
         with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.rename-contigs;
         . = "resources/rename-contigs/ucsc-to-ensembl.txt" )
         " ncbench-workflow/config/config.yaml