small test adjustment

phac-nml · Apr 17, 2024 · b8bf425 · b8bf425
1 parent a1ecbec
commit b8bf425
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diff --git a/.github/scripts/test_nml_nanopore_medaka.sh b/.github/scripts/test_nml_nanopore_medaka.sh
@@ -2,16 +2,16 @@
 set -eo pipefail
 
 # Create a Cache Dir
-mkdir -p conda_cache_dir
+mkdir -p ../conda_cache
 
 ### Run Medaka Pipeline ###
 nextflow run ./main.nf \
     -profile mamba,test \
-    --cache ./conda_cache_dir \
+    --cache ../conda_cache \
     --medaka \
-    --prefix 'nml' \
+    --medaka_model r941_min_hac_g507 \
+    --prefix nml \
     --basecalled_fastq $PWD/.github/data/nanopore/fastq_pass/ \
-    --medakaModel r941_min_hac_g507 \
     --schemeVersion freed_V2_nml \
     --min_length 800 \
     --max_length 1600 \

diff --git a/.github/scripts/test_nml_nanopore_medaka_flat.sh b/.github/scripts/test_nml_nanopore_medaka_flat.sh
@@ -2,16 +2,16 @@
 set -eo pipefail
 
 # Create a Cache Dir
-mkdir -p conda_cache_dir
+mkdir -p ../conda_cache
 
 ### Run Medaka Pipeline Flat ###
 nextflow run ./main.nf \
     -profile mamba,test \
-    --cache ./conda_cache_dir \
+    --cache ../conda_cache \
     --medaka \
-    --prefix 'nml' \
-    --basecalled_fastq $PWD/.github/data/nanopore/fastq_pass/barcode78/ \
     --medaka_model r941_min_hac_g507 \
+    --prefix nml \
+    --basecalled_fastq $PWD/.github/data/nanopore/fastq_pass/barcode78/ \
     --schemeVersion freed_V2_nml \
     --min_length 800 \
     --max_length 1600 \

diff --git a/.github/scripts/test_nml_nanopore_nanopolish.sh b/.github/scripts/test_nml_nanopore_nanopolish.sh
@@ -2,7 +2,7 @@
 set -eo pipefail
 
 # Create a Cache Dir
-mkdir -p conda_cache_dir
+mkdir -p ../conda_cache
 
 # Set if metadata will be used or not for test
 if [ "$1" = "--no_metadata" ]; then
@@ -16,10 +16,10 @@ fi
 ### Run Nanopolish Pipeline ###
 nextflow run ./main.nf \
     -profile mamba,test \
-    --cache ./conda_cache_dir \
+    --cache ../conda_cache \
     $METADATA \
     --nanopolish \
-    --prefix 'nml' \
+    --prefix nml \
     --basecalled_fastq $PWD/.github/data/nanopore/fastq_pass/ \
     --fast5_pass $PWD/.github/data/nanopore/fast5_pass/ \
     --sequencing_summary $PWD/.github/data/nanopore/sequencing_summary.txt \