rm apptainer code

pdimens · May 6, 2024 · d1110ce · d1110ce
1 parent 9e547e8
commit d1110ce
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -98,7 +98,7 @@ jobs:
           pip install dist/*.whl
           resources/buildforCI.sh
       - name: harpy demultiplex
-        run: harpy demultiplex gen1 --snakemake "--apptainer-args sandbox" --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I*
+        run: harpy demultiplex gen1  --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I*
         shell: micromamba-shell {0}
 
   test_preflight:
@@ -130,11 +130,11 @@ jobs:
           resources/buildforCI.sh
       - name: test preflight fastq
         shell: micromamba-shell {0}
-        run: harpy preflight fastq --snakemake "--apptainer-args sandbox" test/fastq
+        run: harpy preflight fastq test/fastq
       - name: test preflight bam
         if: always()
         shell: micromamba-shell {0}
-        run: harpy preflight bam --snakemake "--apptainer-args sandbox" test/bam
+        run: harpy preflight bam test/bam
 
   test_qc:
     needs: [changes, pkgbuild]
@@ -296,7 +296,7 @@ jobs:
         run: harpy snp mpileup -r test/positions.bed -g test/genome/genome.fasta.gz -x "--ignore-RG" test/bam
       - name: snp mpileup-pop
         shell: micromamba-shell {0}
-        run: harpy snp mpileup -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups -s "--apptainer-args sandbox" test/bam
+        run: harpy snp mpileup -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups --snakemake "--show-failed-logs" test/bam
 
   test_freebayes:
     needs: [changes, pkgbuild]
@@ -330,7 +330,7 @@ jobs:
         run: harpy snp freebayes -r test/positions.bed -g test/genome/genome.fasta.gz -x "-g 200" test/bam
       - name: snp freebayes-pop
         shell: micromamba-shell {0}
-        run: harpy snp freebayes -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups test/bam
+        run: harpy snp freebayes -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups --snakemake "--show-failed-logs" test/bam
 
   test_impute:
     needs: [changes, pkgbuild]