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default to conda over container #182

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merged 3 commits into from
Jan 21, 2025
Merged

default to conda over container #182

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044fb03
swap --conda for --container
pdimens Jan 20, 2025
1109d8e
rm container from tests
pdimens Jan 20, 2025
7ffb513
fix handling of "out"
pdimens Jan 21, 2025
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188 changes: 94 additions & 94 deletions .github/workflows/tests.yml
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Expand Up @@ -103,20 +103,20 @@ jobs:
context: .
push: true
tags: pdimens/harpy:latest
- name: Pull Image Locally
id: singularity
shell: micromamba-shell {0}
if: ${{ needs.changes.outputs.modules == 'true' }}
run: |
export APPTAINER_TMPDIR=$PWD/test/
harpy qc --skip-reports --quiet test/fastq/sample1.*.fq.gz
- name: Create Singularity Artifact
if: ${{ steps.singularity.outcome == 'success' }}
uses: actions/upload-artifact@v4
with:
name: deps-image
path: .snakemake/singularity/*.simg
retention-days: 1
# - name: Pull Image Locally
# id: singularity
# shell: micromamba-shell {0}
# if: ${{ needs.changes.outputs.modules == 'true' }}
# run: |
# export APPTAINER_TMPDIR=$PWD/test/
# harpy qc --skip-reports --quiet test/fastq/sample1.*.fq.gz
# - name: Create Singularity Artifact
# if: ${{ steps.singularity.outcome == 'success' }}
# uses: actions/upload-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity/*.simg
# retention-days: 1

dmux_gen1:
needs: [changes, pkgbuild]
Expand Down Expand Up @@ -144,11 +144,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: harpy demultiplex
shell: micromamba-shell {0}
run: harpy demultiplex gen1 --quiet --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I*
Expand Down Expand Up @@ -182,11 +182,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: test preflight fastq
shell: micromamba-shell {0}
run: harpy preflight fastq test/fastq
Expand Down Expand Up @@ -224,11 +224,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: harpy qc
shell: micromamba-shell {0}
run: harpy qc -x "--low_complexity_filter" --quiet test/fastq
Expand Down Expand Up @@ -264,11 +264,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: harpy deconvolve
shell: micromamba-shell {0}
run: harpy deconvolve --quiet test/fastq
Expand Down Expand Up @@ -301,11 +301,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: test bwa
shell: micromamba-shell {0}
run: harpy align bwa --quiet -g test/genome/genome.fasta.gz -x "-A 2" test/fastq
Expand Down Expand Up @@ -339,11 +339,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: test ema
shell: micromamba-shell {0}
run: harpy align ema --quiet --ema-bins 150 -g test/genome/genome.fasta.gz test/fastq
Expand Down Expand Up @@ -377,11 +377,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: test strobealign
shell: micromamba-shell {0}
run: harpy align strobe --quiet -l 125 -g test/genome/genome.fasta.gz test/fastq
Expand Down Expand Up @@ -415,11 +415,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: snp mpileup
shell: micromamba-shell {0}
run: harpy snp mpileup --quiet -r test/positions.bed -g test/genome/genome.fasta.gz -x "--ignore-RG" test/bam
Expand Down Expand Up @@ -456,11 +456,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: snp freebayes
shell: micromamba-shell {0}
run: harpy snp freebayes --quiet -r test/positions.bed -g test/genome/genome.fasta.gz -x "-g 200" test/bam
Expand Down Expand Up @@ -497,11 +497,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: impute
shell: micromamba-shell {0}
run: harpy impute --quiet --vcf test/vcf/test.bcf -p test/stitch.params test/bam
Expand Down Expand Up @@ -539,11 +539,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: phase
shell: micromamba-shell {0}
run: harpy phase --quiet --vcf test/vcf/test.bcf -x "--max_iter 10001" test/bam
Expand Down Expand Up @@ -587,11 +587,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: leviathan
shell: micromamba-shell {0}
run: harpy sv leviathan --quiet -s 100 -b 1 -g test/genome/genome.fasta.gz -x "-M 2002" test/bam
Expand Down Expand Up @@ -630,11 +630,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: naibr
shell: micromamba-shell {0}
run: harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/naibr -x "-min_sv 5000" test/bam_phased && rm -r Genome
Expand Down Expand Up @@ -682,11 +682,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: simulate random snps/indels
shell: micromamba-shell {0}
run: |
Expand Down Expand Up @@ -740,11 +740,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: simulate linked reads
shell: micromamba-shell {0}
run: |
Expand Down Expand Up @@ -780,11 +780,11 @@ jobs:
resources/buildforCI.sh
- name: Clear Space
uses: jlumbroso/free-disk-space@main
- name: Download Singularity Artifact
uses: actions/download-artifact@v4
with:
name: deps-image
path: .snakemake/singularity
# - name: Download Singularity Artifact
# uses: actions/download-artifact@v4
# with:
# name: deps-image
# path: .snakemake/singularity
- name: test assembly
shell: micromamba-shell {0}
run: harpy assembly --quiet -r 4000 test/fastq/sample1.*
Expand Down
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