Try running yq script again

nf-core · Jan 12, 2024 · 06cbad2 · 06cbad2
1 parent aaa52b6
commit 06cbad2
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Showing 2 changed files with 46 additions and 43 deletions.
diff --git a/.github/workflows/ncbench.yml b/.github/workflows/ncbench.yml
@@ -87,36 +87,38 @@ jobs:
       - name: Add entry to config
         uses: mikefarah/yq@master
         env:
-          FASTP_VERSION: ${{ env.FASTP_VERSION }}
+          PIPELINE_VERSION_NO_DOTS: ${{ env.PIPELINE_VERSION_NO_DOTS}}
           PIPELINE_VERSION: ${{ env.PIPELINE_VERSION }}
+          FASTP_VERSION: ${{ env.FASTP_VERSION }}
           BWA_VERSION: ${{ env.BWA_VERSION }}
           GATK_VERSION: ${{ env.GATK_VERSION }}
           STRELKA_VERSION: ${{ env.STRELKA_VERSION }}
           DEPOSITION_ID: ${{ env.DEPOSITION_ID }}
         with:
           # TODO: add in values for all callers, ensure proper extension for the datasets are used.
-          #sh .github/workflows/set_ncbench_config.sh
-          cmd: yq --inplace '
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.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${{ env.STRELKA_VERSION }}" |
-            .genotyping = "none" |
-            .reads = "75M" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.subcategory;
-            . = "NA12878-agilent" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.zenodo;
-            .deposition = ${{ env.DEPOSITION_ID }}  |
-            .filename = "get here proper file names" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.benchmark;
-            . = "giab-NA12878-agilent-75M" ) |
-            with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.rename-contigs;
-            . = "resources/rename-contigs/ucsc-to-ensembl.txt" )
-            '  ncbench-workflow/config/config.yaml
+          cmd: sh .github/workflows/set_ncbench_config.sh
+
+          # yq --inplace '
+          #   with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.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${{ env.STRELKA_VERSION }}" |
+          #   .genotyping = "none" |
+          #   .reads = "75M" ) |
+          #   with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.subcategory;
+          #   . = "NA12878-agilent" ) |
+          #   with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.zenodo;
+          #   .deposition = ${{ env.DEPOSITION_ID }}  |
+          #   .filename = "get here proper file names" ) |
+          #   with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.benchmark;
+          #   . = "giab-NA12878-agilent-75M" ) |
+          #   with(.variant-calls.nf-core-sarek-${{ env.PIPELINE_VERSION_NO_DOTS }}-strelka-agilent-75M.rename-contigs;
+          #   . = "resources/rename-contigs/ucsc-to-ensembl.txt" )
+          #   '  ncbench-workflow/config/config.yaml
 
       - name: Commit files
         run: |

diff --git a/.github/workflows/set_ncbench_config.sh b/.github/workflows/set_ncbench_config.sh
@@ -1,26 +1,27 @@
 #!/bin/bash
 
-        #with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.zenodo;
-        #.deposition = $DEPOSITION_ID  |
-        #.filename = "TODO get here proper file names" ) |
-
-        # .trimming = "FastP v$FASTP_VERSION" |
-        # .read-mapping = "bwa mem v$BWA_VERSION" |
-        # .base-quality-recalibration = "gatk4 v$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" ) |
-
-        #with(.variant-calls.nf-core-sarek-$PIPELINE_VERSION-strelka-agilent-${READS}M.rename-contigs;
-        #. = "resources/rename-contigs/ucsc-to-ensembl.txt" )
-
-
 for READS in 75 200; do
-
+    yq --inplace '
+            with(.variant-calls.nf-core-sarek-${PIPELINE_VERSION_NO_DOTS}-strelka-agilent-75M.labels;
+            .site = "nf-core" |
+            .pipeline = "nf-core/sarek v${PIPELINE_VERSION}" |
+            .trimming = "FastP v${FASTP_VERSION }" |
+            .read-mapping = "bwa mem v${ BWA_VERSION }" |
+            .base-quality-recalibration = "gatk4 v${ GATK_VERSION }" |ß
+            .realignment = "none" |
+            .variant-detection  = "strelka2 v${ STRELKA_VERSION }" |
+            .genotyping = "none" |
+            .reads = "75M" ) |
+            with(.variant-calls.nf-core-sarek-${ PIPELINE_VERSION_NO_DOTS }-strelka-agilent-75M.subcategory;
+            . = "NA12878-agilent" ) |
+            with(.variant-calls.nf-core-sarek-${ PIPELINE_VERSION_NO_DOTS }-strelka-agilent-75M.zenodo;
+            .deposition = ${ DEPOSITION_ID }  |
+            .filename = "get here proper file names" ) |
+            with(.variant-calls.nf-core-sarek-${ PIPELINE_VERSION_NO_DOTS }-strelka-agilent-75M.benchmark;
+            . = "giab-NA12878-agilent-75M" ) |
+            with(.variant-calls.nf-core-sarek-${ PIPELINE_VERSION_NO_DOTS }-strelka-agilent-75M.rename-contigs;
+            . = "resources/rename-contigs/ucsc-to-ensembl.txt" )
+            '  ncbench-workflow/config/config.yaml
 done