From f668217dbf87b39010a4e734626b9b64b54a8964 Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Thu, 11 Jan 2024 14:46:18 +0000
Subject: [PATCH] use run instead to loop over read numbers

---
 .github/workflows/ncbench.yml | 51 ++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/ncbench.yml b/.github/workflows/ncbench.yml
index 315f2f09e0..62efb4ebe1 100644
--- a/.github/workflows/ncbench.yml
+++ b/.github/workflows/ncbench.yml
@@ -80,32 +80,33 @@ jobs:
 
       - name: Add entry to config
         uses: mikefarah/yq@master
-        with:
-          # TODO: add in values for all callers, ensure proper extension for the datasets are used.
-          # TODO check if trimming should be enabled actually
-          cmd: for reads in 75 200; do
+        #with:
+        # TODO: add in values for all callers, ensure proper extension for the datasets are used.
+        # TODO check if trimming should be enabled actually
+        run: |
+          for reads in 75 200; do
             yq --inplace '
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.labels;
-            .site = "nf-core" |
-            .pipeline = "nf-core/sarek v${{ env.PIPELINE_VERSION }}" |
-            .trimming = "FastP v${{ env.FASTP_VERSION }}" |
-            .read-mapping = "bwa mem v${{ env.BWA_VERSION }}" |
-            .base-quality-recalibration = "gatk4 v${{ env.GATK_VERSION }}" |
-            .realignment = "none" |
-            .variant-detection  = "strelka2 v${{ env.STRELKA_VERSION }}" |
-            .genotyping = "none" |
-            .reads = "${reads}M" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.subcategory;
-            . = "NA12878-agilent" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.zenodo;
-            .deposition = $DEPOSITION_ID  |
-            .filename = "TODO get here proper file names" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.benchmark;
-            . = "giab-NA12878-agilent-${reads}M" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.rename-contigs;
-            . = "resources/rename-contigs/ucsc-to-ensembl.txt" )
-            ' ncbench-workflow/config/config.yaml
-            done
+              with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.labels;
+              .site = "nf-core" |
+              .pipeline = "nf-core/sarek v${{ env.PIPELINE_VERSION }}" |
+              .trimming = "FastP v${{ env.FASTP_VERSION }}" |
+              .read-mapping = "bwa mem v${{ env.BWA_VERSION }}" |
+              .base-quality-recalibration = "gatk4 v${{ env.GATK_VERSION }}" |
+              .realignment = "none" |
+              .variant-detection  = "strelka2 v${{ env.STRELKA_VERSION }}" |
+              .genotyping = "none" |
+              .reads = "${reads}M" ) |
+              with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.subcategory;
+              . = "NA12878-agilent" ) |
+              with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.zenodo;
+              .deposition = $DEPOSITION_ID  |
+              .filename = "TODO get here proper file names" ) |
+              with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.benchmark;
+              . = "giab-NA12878-agilent-${reads}M" ) |
+              with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION }}-strelka-agilent-${reads}M.rename-contigs;
+              . = "resources/rename-contigs/ucsc-to-ensembl.txt" )
+              ' ncbench-workflow/config/config.yaml
+          done
 
       # TODO: enable using secrets here
       - name: Commit files