specify apptainer

pdimens · May 6, 2024 · 0f37184 · 0f37184
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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 --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I*
+        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*
         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 test/fastq
+        run: harpy preflight fastq --snakemake "--apptainer-args sandbox" test/fastq
       - name: test preflight bam
         if: always()
         shell: micromamba-shell {0}
-        run: harpy preflight bam test/bam
+        run: harpy preflight bam --snakemake "--apptainer-args sandbox" test/bam
 
   test_qc:
     needs: [changes, pkgbuild]
@@ -165,11 +165,11 @@ jobs:
           resources/buildforCI.sh
       - name: harpy qc
         shell: micromamba-shell {0}
-        run: harpy qc -x "--trim_poly_g"  --snakemake "--show-failed-logs" test/fastq
+        run: harpy qc -x "--trim_poly_g"  --snakemake "--show-failed-logs --apptainer-args sandbox" test/fastq
       - name: harpy qc skip adapter trimming
         if: always()
         shell: micromamba-shell {0}
-        run: harpy qc -a --snakemake "--show-failed-logs" test/fastq
+        run: harpy qc -a --snakemake "--show-failed-logs --apptainer-args sandbox" test/fastq
 
   test_bwa:
     needs: [changes, pkgbuild]
@@ -200,7 +200,7 @@ jobs:
           resources/buildforCI.sh
       - name: test bwa
         shell: micromamba-shell {0}
-        run: harpy align bwa -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" -x "-A 2" test/fastq
+        run: harpy align bwa -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-A 2" test/fastq
 
   test_ema:
     needs: [changes, pkgbuild]
@@ -231,7 +231,7 @@ jobs:
           resources/buildforCI.sh
       - name: test ema
         shell: micromamba-shell {0}
-        run: harpy align ema --ema-bins 150 -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" -x "-d" test/fastq
+        run: harpy align ema --ema-bins 150 -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-d" test/fastq
 
   test_minimap:
     needs: [changes, pkgbuild]
@@ -262,7 +262,7 @@ jobs:
           resources/buildforCI.sh
       - name: test minimap
         shell: micromamba-shell {0}
-        run: harpy align minimap -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" -x "--seed 13" test/fastq
+        run: harpy align minimap -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "--seed 13" test/fastq
 
   test_mpileup:
     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 test/bam
+        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
 
   test_freebayes:
     needs: [changes, pkgbuild]
@@ -361,11 +361,11 @@ jobs:
           resources/buildforCI.sh
       - name: impute
         shell: micromamba-shell {0}
-        run: harpy impute --vcf test/vcf/test.bcf -p test/stitch.params --snakemake "--show-failed-logs" test/bam
+        run: harpy impute --vcf test/vcf/test.bcf -p test/stitch.params --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam
       - name: impute from vcf
         shell: micromamba-shell {0}
         if: always()
-        run: harpy impute --vcf-samples -o vcfImpute --vcf test/vcf/test.bcf -p test/stitch.params --snakemake "--show-failed-logs" test/bam
+        run: harpy impute --vcf-samples -o vcfImpute --vcf test/vcf/test.bcf -p test/stitch.params --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam
 
   test_phase:
     needs: [changes, pkgbuild]
@@ -396,15 +396,15 @@ jobs:
           resources/buildforCI.sh
       - name: phase
         shell: micromamba-shell {0}
-        run: harpy phase --vcf test/vcf/test.bcf --snakemake "--show-failed-logs" -x "--max_iter 10001" test/bam
+        run: harpy phase --vcf test/vcf/test.bcf --snakemake "--show-failed-logs --apptainer-args sandbox" -x "--max_iter 10001" test/bam
       - name: phase with indels
         shell: micromamba-shell {0}
         if: always()
-        run: harpy phase --vcf test/vcf/test.bcf -o phaseindel -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" test/bam
+        run: harpy phase --vcf test/vcf/test.bcf -o phaseindel -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam
       - name: phase from vcf
         shell: micromamba-shell {0}
         if: always()
-        run: harpy phase --vcf-samples -o phasevcf --vcf test/vcf/test.bcf --snakemake "--show-failed-logs" test/bam
+        run: harpy phase --vcf-samples -o phasevcf --vcf test/vcf/test.bcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam
 
   test_leviathan:
     needs: [changes, pkgbuild]
@@ -435,12 +435,12 @@ jobs:
           resources/buildforCI.sh
       - name: leviathan
         shell: micromamba-shell {0}
-        run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs" -x "-M 2002" test/bam
+        run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-M 2002" test/bam
         continue-on-error: true
       - name: leviathan-pop
         if: always()
         shell: micromamba-shell {0}
-        run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz -o SV/leviathanpop -p test/samples.groups --snakemake "--show-failed-logs" test/bam
+        run: harpy sv leviathan -n 100 -b 1 -g test/genome/genome.fasta.gz -o SV/leviathanpop -p test/samples.groups --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam
 
   test_naibr:
     needs: [changes, pkgbuild]
@@ -471,20 +471,20 @@ jobs:
           resources/buildforCI.sh
       - name: naibr
         shell: micromamba-shell {0}
-        run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/naibr --snakemake "--show-failed-logs" -x "-min_sv 5000" test/bam_phased && rm -r Genome
+        run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/naibr --snakemake "--show-failed-logs --apptainer-args sandbox" -x "-min_sv 5000" test/bam_phased && rm -r Genome
       - name: naibr pop
         if: always()
         shell: micromamba-shell {0}
-        run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/pop -p test/samples.groups --snakemake "--show-failed-logs" test/bam_phased && rm -r Genome
+        run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/pop -p test/samples.groups --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam_phased && rm -r Genome
       - name: naibr with phasing
         if: always()
         shell: micromamba-shell {0}
         run: |
-          harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phase -v test/vcf/test.phased.bcf --snakemake "--show-failed-logs" test/bam && rm -r Genome
+          harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phase -v test/vcf/test.phased.bcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam && rm -r Genome
       - name: naibr pop with phasing
         if: always()
         shell: micromamba-shell {0}
-        run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phasepop -v test/vcf/test.phased.bcf -p test/samples.groups --snakemake "--show-failed-logs" test/bam && rm -r Genome
+        run: harpy sv naibr -g test/genome/genome.fasta.gz -o SV/phasepop -v test/vcf/test.phased.bcf -p test/samples.groups --snakemake "--show-failed-logs --apptainer-args sandbox" test/bam && rm -r Genome
 
 
   test_simulate_variants:
@@ -517,26 +517,26 @@ jobs:
       - name: simulate random snps/indels
         shell: micromamba-shell {0}
         run: |
-          harpy simulate snpindel --snp-count 10 --indel-count 10 -z 0.5 --snakemake "--show-failed-logs" test/genome/genome.fasta.gz
-          harpy simulate snpindel --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/sim.snpindel.snp.hap1.vcf --indel-vcf Simulate/snpindel/sim.snpindel.indel.hap1.vcf --snakemake "--show-failed-logs" test/genome/genome.fasta.gz
+          harpy simulate snpindel --snp-count 10 --indel-count 10 -z 0.5 --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
+          harpy simulate snpindel --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/sim.snpindel.snp.hap1.vcf --indel-vcf Simulate/snpindel/sim.snpindel.indel.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
       - name: simulate inversions
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate inversion --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate inversion --prefix Simulate/invvcf --vcf Simulate/inversion/sim.inversion.hap1.vcf --snakemake "--show-failed-logs" test/genome/genome.fasta.gz
+          harpy simulate inversion --prefix Simulate/invvcf --vcf Simulate/inversion/sim.inversion.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
       - name: simulate cnv
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate cnv --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate cnv --prefix Simulate/cnvvcf --vcf Simulate/cnv/sim.cnv.hap1.vcf --snakemake "--show-failed-logs" test/genome/genome.fasta.gz
+          harpy simulate cnv --prefix Simulate/cnvvcf --vcf Simulate/cnv/sim.cnv.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
       - name: simulate translocations
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate translocation --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate translocation --prefix Simulate/transvcf --vcf Simulate/translocation/sim.translocation.hap1.vcf --snakemake "--show-failed-logs" test/genome/genome.fasta.gz
+          harpy simulate translocation --prefix Simulate/transvcf --vcf Simulate/translocation/sim.translocation.hap1.vcf --snakemake "--show-failed-logs --apptainer-args sandbox" test/genome/genome.fasta.gz
 
   test_simulate_linkedreads:
     needs: [changes, pkgbuild]
@@ -567,7 +567,7 @@ jobs:
           resources/buildforCI.sh
       - name: simulate linked reads
         shell: micromamba-shell {0}
-        run: harpy simulate linkedreads --snakemake "--show-failed-logs" -t 4 -n 2  -l 100 -p 50 test/genome/genome.fasta.gz test/genome/genome2.fasta.gz
+        run: harpy simulate linkedreads --snakemake "--show-failed-logs --apptainer-args sandbox" -t 4 -n 2  -l 100 -p 50 test/genome/genome.fasta.gz test/genome/genome2.fasta.gz
 
   test_extras:
     needs: [changes, pkgbuild]

diff --git a/src/harpy/align.py b/src/harpy/align.py
@@ -33,7 +33,7 @@ def bwa(input, output_dir, genome, threads, extra_params, quality_filter, molecu
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --use-apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/align-bwa.smk')
     command.append("--configfile")
@@ -104,7 +104,7 @@ def ema(input, output_dir, platform, whitelist, genome, threads, ema_bins, skipr
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --use-apptainer --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/align-ema.smk')
     command.append("--configfile")
@@ -188,7 +188,7 @@ def minimap(input, output_dir, genome, threads, extra_params, quality_filter, mo
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --use-apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/align-minimap.smk')
     command.append("--configfile")

diff --git a/src/harpy/demultiplex.py b/src/harpy/demultiplex.py
@@ -28,7 +28,7 @@ def gen1(r1_fq, r2_fq, i1_fq, i2_fq, output_dir, schema, threads, snakemake, ski
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --use-apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/demultiplex.gen1.smk')
     command.append("--configfile")

diff --git a/src/harpy/impute.py b/src/harpy/impute.py
@@ -37,7 +37,7 @@ def impute(input, output_dir, parameters, threads, vcf, vcf_samples, extra_param
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --use-apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/impute.smk')
     command.append("--configfile")

diff --git a/src/harpy/phase.py b/src/harpy/phase.py
@@ -36,7 +36,7 @@ def phase(input, output_dir, vcf, threads, molecule_distance, prune_threshold, v
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --use-apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f"{workflowdir}/phase.smk")
     command.append("--configfile")

diff --git a/src/harpy/preflight.py b/src/harpy/preflight.py
@@ -82,7 +82,7 @@ def bam(input, output_dir, threads, snakemake, quiet, print_only):
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock --software-deployment-method conda apptainer --use-apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/preflight-bam.smk')
     command.append('--configfile')

diff --git a/src/harpy/qc.py b/src/harpy/qc.py
@@ -33,7 +33,7 @@ def qc(input, output_dir, min_length, max_length, ignore_adapters, extra_params,
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock  --software-deployment-method conda apptainer apptainer --conda-prefix .snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock  --software-deployment-method conda apptainer --use-apptainer apptainer --conda-prefix .snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/qc.smk')
     command.append('--configfile')

diff --git a/src/harpy/simulatelinkedreads.py b/src/harpy/simulatelinkedreads.py
@@ -34,7 +34,7 @@ def linkedreads(genome_hap1, genome_hap2, output_dir, outer_distance, distance_s
     """
     output_dir = output_dir.rstrip("/")
     workflowdir = f"{output_dir}/workflow"
-    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock  --software-deployment-method conda apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
+    command = f'snakemake --rerun-incomplete --rerun-triggers input mtime params --nolock  --software-deployment-method conda apptainer --use-apptainer --conda-prefix ./.snakemake/conda --cores {threads} --directory .'.split()
     command.append('--snakefile')
     command.append(f'{workflowdir}/simulate-linkedreads.smk')
     command.append('--configfile')