run eager test outside pipeline

ktmeaton · Jun 18, 2020 · 108a90a · 108a90a
1 parent 331bf04
commit 108a90a
Showing 1 changed file with 22 additions and 8 deletions.
diff --git a/.github/workflows/sra.yaml b/.github/workflows/sra.yaml
@@ -52,12 +52,12 @@ jobs:
           cp ~/.nextflow/assets/nf-core/eager/assets/multiqc_config.yaml \
              ./multiqc_config_custom.yaml;
 
-      - name: perl5lib Setup
-        shell: bash -l {0}
-        run: |
-          echo $PERL5LIB
-          export PERL5LIB=~/miniconda3/envs/phylo-env/lib/site_perl/5.26.2/:$PERL5LIB
-          echo $PERL5LIB
+      #- name: perl5lib Setup
+      #  shell: bash -l {0}
+      #  run: |
+      #    echo $PERL5LIB
+      #    export PERL5LIB=~/miniconda3/envs/phylo-env/lib/site_perl/5.26.2/:$PERL5LIB
+      #    echo $PERL5LIB
 
       # Test the SRA EAGER Pipeline
       - name: sra download
@@ -76,8 +76,22 @@ jobs:
       - name: eager test
         shell: bash -l {0}
         run: |
-          ls -l test/
-          ls -l test/sra_download/fastq/*
+          conda activate nf-core-eager-2.2.0dev
+          nextflow run nf-core/eager -r dev \
+            --input test/sqlite_import/metadata_sra_eager.tsv \
+            --outdir test/eager \
+            --fasta test/reference_genome/GCF_000009065.1_ASM906v1_genomic.fna \
+            --multiqc_config multiqc_config_custom.yaml \
+            --clip_readlength 35 \
+            --preserve5p \
+            --mergedonly \
+            --mapper bwaaln \
+            --bwaalnn 0.01 \
+            --bwaalnl 16 \
+            --run_bam_filtering \
+            --bam_mapping_quality_threshold 30 \
+            --bam_discard_unmapped \
+            --bam_unmapped_type discard;
 
       # Artifact uploads
       - name: artifact SQLite import