From ee2373473fec6a4d510d1fa323aec21a560e3acd Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 12:15:40 +0100 Subject: [PATCH 01/15] fix: distinguish soft and hard AF filter --- juno_mapping.py | 20 +++++++--- workflow/rules/qc_variant_calling.smk | 2 +- workflow/rules/variant_filtering.smk | 54 ++++++++++++++++++++------- 3 files changed, 57 insertions(+), 19 deletions(-) diff --git a/juno_mapping.py b/juno_mapping.py index 7317c93..742c3ff 100644 --- a/juno_mapping.py +++ b/juno_mapping.py @@ -145,12 +145,20 @@ def _add_args_to_parser(self) -> None: help="Minimum length for fastq reads to be kept after trimming.", ) self.add_argument( - "-maf", - "--minimum-allele-frequency", + "-smaf", + "--soft-filter-minimum-allele-frequency", type=check_number_within_range(minimum=0, maximum=1), metavar="FLOAT", default=0.8, - help="Minimum allele frequency to filter variants on.", + help="Minimum allele frequency to soft filter variants on. Soft filtering is done by adding a filter tag to the VCF file.", + ) + self.add_argument( + "-hmaf", + "--hard-filter-minimum-allele-frequency", + type=check_number_within_range(minimum=0, maximum=1), + metavar="FLOAT", + default=0.2, + help="Minimum allele frequency to hard filter variants on. Hard filtering is done by removing variants from the VCF file.", ) self.add_argument( "--min-reads-per-strand", @@ -176,7 +184,8 @@ def _parse_args(self) -> argparse.Namespace: self.time_limit: int = args.time_limit self.species: str = args.species self.minimum_depth_variant: int = args.minimum_depth_variant - self.minimum_allele_frequency: float = args.minimum_allele_frequency + self.hard_filter_minimum_allele_frequency: float = args.hard_filter_minimum_allele_frequency + self.soft_filter_minimum_allele_frequency: float = args.soft_filter_minimum_allele_frequency self.min_reads_per_strand: int = args.min_reads_per_strand return args @@ -258,7 +267,8 @@ def setup(self) -> None: "use_singularity": str(self.snakemake_args["use_singularity"]), "species": str(self.species), "minimum_depth": int(self.minimum_depth_variant), - "minimum_allele_frequency": float(self.minimum_allele_frequency), + "soft_filter_minimum_allele_frequency": float(self.soft_filter_minimum_allele_frequency), + "hard_filter_minimum_allele_frequency": float(self.hard_filter_minimum_allele_frequency), "min_reads_per_strand": int(self.min_reads_per_strand), } diff --git a/workflow/rules/qc_variant_calling.smk b/workflow/rules/qc_variant_calling.smk index 5c17575..ae18f0c 100644 --- a/workflow/rules/qc_variant_calling.smk +++ b/workflow/rules/qc_variant_calling.smk @@ -1,6 +1,6 @@ rule get_filter_status: input: - vcf=OUT + "/variants_raw/FMC_af_depth_masked/{sample}.vcf", + vcf=OUT + "/variants/{sample}.vcf", output: tsv=OUT + "/qc_variant_calling/get_filter_status/{sample}.tsv", message: diff --git a/workflow/rules/variant_filtering.smk b/workflow/rules/variant_filtering.smk index af6a84c..d687862 100644 --- a/workflow/rules/variant_filtering.smk +++ b/workflow/rules/variant_filtering.smk @@ -29,13 +29,41 @@ gatk FilterMutectCalls -V {input.vcf} \ """ -rule filter_af: +rule hard_filter_af: input: vcf=OUT + "/variants_raw/FMC/{sample}.vcf", - stats=OUT + "/variants_raw/raw/{sample}.vcf.stats", ref=OUT + "/reference/reference.fasta", output: - vcf=OUT + "/variants_raw/FMC_af/{sample}.vcf", + vcf=OUT + "/variants_raw/FMC_afhard/{sample}.vcf", + message: + "Hard filtering variants with very low allele frequency for {wildcards.sample}" + container: + "docker://staphb/bcftools:1.16" + conda: + "../envs/bcftools.yaml" + params: + min_af=config["hard_filter_minimum_allele_frequency"], + log: + OUT + "/log/hard_filter_af/{sample}.log", + threads: config["threads"]["filter_variants"] + resources: + mem_gb=config["mem_gb"]["filter_variants"], + shell: + """ +bcftools filter \ +--exclude \"FORMAT/AF < {params.min_af}\" \ +{input.vcf} \ +1>{output.vcf} \ +2>{log} + """ + + +rule soft_filter_af: + input: + vcf=OUT + "/variants_raw/FMC_afhard/{sample}.vcf", + ref=OUT + "/reference/reference.fasta", + output: + vcf=OUT + "/variants_raw/FMC_afhard_afsoft/{sample}.vcf", message: "Marking minority variants for {wildcards.sample}" container: @@ -43,7 +71,7 @@ rule filter_af: conda: "../envs/bcftools.yaml" params: - min_af=config["minimum_allele_frequency"], + min_af=config["soft_filter_minimum_allele_frequency"], log: OUT + "/log/filter_af/{sample}.log", threads: config["threads"]["filter_variants"] @@ -62,10 +90,10 @@ bcftools filter \ rule filter_depth: input: - vcf=OUT + "/variants_raw/FMC_af/{sample}.vcf", + vcf=OUT + "/variants_raw/FMC_afhard_afsoft/{sample}.vcf", ref=OUT + "/reference/reference.fasta", output: - vcf=OUT + "/variants_raw/FMC_af_depth/{sample}.vcf", + vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth/{sample}.vcf", container: "docker://staphb/bcftools:1.16" conda: @@ -103,11 +131,11 @@ if config["disable_mask"] == "True": rule filter_mask: input: - vcf=OUT + "/variants_raw/FMC_af_depth/{sample}.vcf", + vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth/{sample}.vcf", ref=OUT + "/reference/reference.fasta", mask=OUT + "/variants_raw/no_mask.bed", output: - vcf=OUT + "/variants_raw/FMC_af_depth_masked/{sample}.vcf", + vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth_masked/{sample}.vcf", log: OUT + "/log/filter_depth/{sample}.log", threads: config["threads"]["filter_variants"] @@ -138,11 +166,11 @@ else: rule filter_mask: input: - vcf=OUT + "/variants_raw/FMC_af_depth/{sample}.vcf", + vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth/{sample}.vcf", ref=OUT + "/reference/reference.fasta", mask=OUT + "/variants_raw/mask.bed", output: - vcf=OUT + "/variants_raw/FMC_af_depth_masked/{sample}.vcf", + vcf=OUT + "/variants/{sample}.vcf", container: "docker://staphb/bcftools:1.16" conda: @@ -165,10 +193,10 @@ bcftools filter \ rule remove_low_confidence_variants: input: - vcf=OUT + "/variants_raw/FMC_af_depth_masked/{sample}.vcf", + vcf=OUT + "/variants/{sample}.vcf", ref=OUT + "/reference/reference.fasta", output: - vcf=OUT + "/variants/{sample}.vcf", + vcf=OUT + "/variants_clean/{sample}.vcf", message: "Remove low confidence variants for {wildcards.sample}" conda: @@ -193,7 +221,7 @@ gatk SelectVariants \ rule select_snps: input: ref=OUT + "/reference/reference.fasta", - vcf=OUT + "/variants/{sample}.vcf", + vcf=OUT + "/variants_clean/{sample}.vcf", output: vcf=OUT + "/variants_snps_only/{sample}.snps.vcf", container: From fceb00a07c324e37286e9574ebd0a1fdcd5b7c42 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 12:28:56 +0100 Subject: [PATCH 02/15] style: black formatting --- juno_mapping.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/juno_mapping.py b/juno_mapping.py index 742c3ff..e3f013a 100644 --- a/juno_mapping.py +++ b/juno_mapping.py @@ -184,8 +184,12 @@ def _parse_args(self) -> argparse.Namespace: self.time_limit: int = args.time_limit self.species: str = args.species self.minimum_depth_variant: int = args.minimum_depth_variant - self.hard_filter_minimum_allele_frequency: float = args.hard_filter_minimum_allele_frequency - self.soft_filter_minimum_allele_frequency: float = args.soft_filter_minimum_allele_frequency + self.hard_filter_minimum_allele_frequency: float = ( + args.hard_filter_minimum_allele_frequency + ) + self.soft_filter_minimum_allele_frequency: float = ( + args.soft_filter_minimum_allele_frequency + ) self.min_reads_per_strand: int = args.min_reads_per_strand return args @@ -267,8 +271,12 @@ def setup(self) -> None: "use_singularity": str(self.snakemake_args["use_singularity"]), "species": str(self.species), "minimum_depth": int(self.minimum_depth_variant), - "soft_filter_minimum_allele_frequency": float(self.soft_filter_minimum_allele_frequency), - "hard_filter_minimum_allele_frequency": float(self.hard_filter_minimum_allele_frequency), + "soft_filter_minimum_allele_frequency": float( + self.soft_filter_minimum_allele_frequency + ), + "hard_filter_minimum_allele_frequency": float( + self.hard_filter_minimum_allele_frequency + ), "min_reads_per_strand": int(self.min_reads_per_strand), } From 8e8a8500635db7608a6f9d585cb3ba3d13db3e99 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 12:35:00 +0100 Subject: [PATCH 03/15] fix: fix paths when not masking regions --- workflow/rules/variant_filtering.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/variant_filtering.smk b/workflow/rules/variant_filtering.smk index d687862..e84366a 100644 --- a/workflow/rules/variant_filtering.smk +++ b/workflow/rules/variant_filtering.smk @@ -135,7 +135,7 @@ if config["disable_mask"] == "True": ref=OUT + "/reference/reference.fasta", mask=OUT + "/variants_raw/no_mask.bed", output: - vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth_masked/{sample}.vcf", + vcf=OUT + "/variants/{sample}.vcf", log: OUT + "/log/filter_depth/{sample}.log", threads: config["threads"]["filter_variants"] From 93aa11c7c1fd8a9db3b057382a51a4a817682929 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 14:37:24 +0100 Subject: [PATCH 04/15] ci: test extra space --- .github/workflows/juno_mapping_singularity.yaml | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index bb8a563..2f5328d 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -18,6 +18,16 @@ jobs: name: Singularity Juno_mapping pipeline ${{ matrix.config.os }} steps: + - name: check space 1 + shell: bash -l {0} + run: | + df -h . + - name: Maximize build space + uses: easimon/maximize-build-space@master + with: + root-reserve-mb: 512 + swap-size-mb: 1024 + remove-dotnet: 'true' - uses: actions/checkout@v2 - uses: eWaterCycle/setup-singularity@v7 with: @@ -45,7 +55,7 @@ jobs: - name: Conda list shell: bash -l {0} run: conda list - - name: check space + - name: check space 2 shell: bash -l {0} run: | which singularity @@ -65,7 +75,7 @@ jobs: - name: Test the juno_mapping wrapper shell: bash -l {0} run: pytest -v tests/test_juno_mapping.py - - name: check space 2 + - name: check space 3 if: always() shell: bash -l {0} run: | From 68f9caf401b04b8be731d80a3c784359e92ef871 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 15:38:05 +0100 Subject: [PATCH 05/15] ci: use runner space differently --- .../workflows/juno_mapping_singularity.yaml | 25 +++++++++++-------- tests/test_pipeline_singularity.py | 4 +-- 2 files changed, 16 insertions(+), 13 deletions(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index 2f5328d..4b05fec 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -5,7 +5,7 @@ name: Singularity e2e test on: [pull_request] env: - KRAKEN_DEFAULT_DB: /home/runner/kraken-database + KRAKEN_DEFAULT_DB: /mnt/kraken-database jobs: singularity_end_to_end: @@ -21,23 +21,21 @@ jobs: - name: check space 1 shell: bash -l {0} run: | + echo "Checking space: ." df -h . - - name: Maximize build space - uses: easimon/maximize-build-space@master - with: - root-reserve-mb: 512 - swap-size-mb: 1024 - remove-dotnet: 'true' - - uses: actions/checkout@v2 + echo "Checking space: /mnt" + df -h /mnt + - uses: actions/checkout@v4 - uses: eWaterCycle/setup-singularity@v7 with: - singularity-version: 3.8.7 + singularity-version: 3.8.3 - name: Install Conda environment with Micromamba uses: mamba-org/setup-micromamba@v1 with: generate-run-shell: false # see https://github.com/mamba-org/setup-micromamba/issues/130 cache-downloads: true environment-file: envs/juno_mapping.yaml + environment-path: /mnt/juno_mapping - name: Cache minikraken id: cache-minikraken uses: actions/cache@v3 @@ -52,6 +50,7 @@ jobs: curl -k https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20220908.tar.gz > k2_viral_20220908.tar.gz tar zxvf k2_viral_20220908.tar.gz ls -lh + rm k2_viral_20220908.tar.gz - name: Conda list shell: bash -l {0} run: conda list @@ -66,7 +65,10 @@ jobs: sudo rm -rf /opt/ghc sudo rm -rf "/usr/local/share/boost" fi + echo "Checking space: ." df -h . + echo "Checking space: /mnt" + df -h /mnt which singularity singularity --version - name: Test juno_mapping pipeline using singularity. @@ -79,6 +81,7 @@ jobs: if: always() shell: bash -l {0} run: | + echo "Checking space: ." df -h . - - \ No newline at end of file + echo "Checking space: /mnt" + df -h /mnt \ No newline at end of file diff --git a/tests/test_pipeline_singularity.py b/tests/test_pipeline_singularity.py index ef0e2e3..d8d5689 100644 --- a/tests/test_pipeline_singularity.py +++ b/tests/test_pipeline_singularity.py @@ -43,7 +43,7 @@ class TestJunoMappingPipelineSingularity(unittest.TestCase): 46679: {"REF": "C", "ALT": "G"}, } - output_dir = Path("pipeline_test_output_singularity") + output_dir = Path("/mnt/pipeline_test_output_singularity") input_dir = "tests" @classmethod @@ -81,7 +81,7 @@ def test_010_junomapping_run_in_singularity(self) -> None: "--db-dir", str(kraken_db), "--prefix", - "/home/runner/sing_containers", + "/mnt/sing_containers", ] ) pipeline.run() From 2334bb415ab2243530e67f6f7c2e1c24f36c76d5 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 15:50:23 +0100 Subject: [PATCH 06/15] ci: set permissions on mnt --- .github/workflows/juno_mapping_singularity.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index 4b05fec..439936f 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -21,6 +21,7 @@ jobs: - name: check space 1 shell: bash -l {0} run: | + sudo chmod -R 777 /mnt echo "Checking space: ." df -h . echo "Checking space: /mnt" From aa0068f27b983ddbad06000ec658b86ef9f06375 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 16:09:02 +0100 Subject: [PATCH 07/15] ci: fix k2 db path --- tests/test_pipeline_singularity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_pipeline_singularity.py b/tests/test_pipeline_singularity.py index d8d5689..92cf9c5 100644 --- a/tests/test_pipeline_singularity.py +++ b/tests/test_pipeline_singularity.py @@ -61,7 +61,7 @@ def test_010_junomapping_run_in_singularity(self) -> None: kraken_db = Path.home().joinpath("kraken-database") assert kraken_db.exists(), "Kraken database not found" else: - kraken_db = Path("/home/runner/kraken-database") + kraken_db = Path("/mnt/kraken-database") pipeline = JunoMapping( argv=[ From 8f12a2156c6189117153df7f6df7699a0185a52f Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 16:31:54 +0100 Subject: [PATCH 08/15] ci: check storage --- .github/workflows/juno_mapping_singularity.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index 439936f..67bb033 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -26,6 +26,9 @@ jobs: df -h . echo "Checking space: /mnt" df -h /mnt + echo "Checking dir sizes" + du -sh * + du -sh */* - uses: actions/checkout@v4 - uses: eWaterCycle/setup-singularity@v7 with: @@ -70,6 +73,9 @@ jobs: df -h . echo "Checking space: /mnt" df -h /mnt + echo "Checking dir sizes" + du -sh * + du -sh */* which singularity singularity --version - name: Test juno_mapping pipeline using singularity. @@ -85,4 +91,7 @@ jobs: echo "Checking space: ." df -h . echo "Checking space: /mnt" - df -h /mnt \ No newline at end of file + df -h /mnt + echo "Checking dir sizes" + du -sh * + du -sh */* \ No newline at end of file From 787c360ff4f5210bf94df44893d3a4d19ad19390 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 16:41:13 +0100 Subject: [PATCH 09/15] ci: test --- .github/workflows/juno_mapping_singularity.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index 67bb033..0a4996b 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -27,8 +27,8 @@ jobs: echo "Checking space: /mnt" df -h /mnt echo "Checking dir sizes" - du -sh * - du -sh */* + du -sh /* + du -sh /*/* - uses: actions/checkout@v4 - uses: eWaterCycle/setup-singularity@v7 with: @@ -74,8 +74,8 @@ jobs: echo "Checking space: /mnt" df -h /mnt echo "Checking dir sizes" - du -sh * - du -sh */* + du -sh /* + du -sh /*/* which singularity singularity --version - name: Test juno_mapping pipeline using singularity. @@ -93,5 +93,5 @@ jobs: echo "Checking space: /mnt" df -h /mnt echo "Checking dir sizes" - du -sh * - du -sh */* \ No newline at end of file + du -sh /* + du -sh /*/* \ No newline at end of file From bdacc55afe63cd27737748f8497e66a73e1bd786 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 16:52:53 +0100 Subject: [PATCH 10/15] ci: test which dirs use lot of space --- .github/workflows/juno_mapping_singularity.yaml | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index 0a4996b..3ca4d02 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -26,9 +26,6 @@ jobs: df -h . echo "Checking space: /mnt" df -h /mnt - echo "Checking dir sizes" - du -sh /* - du -sh /*/* - uses: actions/checkout@v4 - uses: eWaterCycle/setup-singularity@v7 with: @@ -39,7 +36,7 @@ jobs: generate-run-shell: false # see https://github.com/mamba-org/setup-micromamba/issues/130 cache-downloads: true environment-file: envs/juno_mapping.yaml - environment-path: /mnt/juno_mapping + create-args: --prefix /mnt/juno_mapping - name: Cache minikraken id: cache-minikraken uses: actions/cache@v3 @@ -73,9 +70,6 @@ jobs: df -h . echo "Checking space: /mnt" df -h /mnt - echo "Checking dir sizes" - du -sh /* - du -sh /*/* which singularity singularity --version - name: Test juno_mapping pipeline using singularity. @@ -92,6 +86,6 @@ jobs: df -h . echo "Checking space: /mnt" df -h /mnt - echo "Checking dir sizes" - du -sh /* - du -sh /*/* \ No newline at end of file + du -sh /mnt/juno_mapping + du -sh /mnt/kraken-database + du -sh ${{ env.GITHUB_WORKSPACE }} \ No newline at end of file From 7d5ed415ab66fbd4914ffe286a1b010940b998f3 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 16:56:17 +0100 Subject: [PATCH 11/15] ci: revert mamba location setting --- .github/workflows/juno_mapping_singularity.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index 3ca4d02..c3dd571 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -36,7 +36,6 @@ jobs: generate-run-shell: false # see https://github.com/mamba-org/setup-micromamba/issues/130 cache-downloads: true environment-file: envs/juno_mapping.yaml - create-args: --prefix /mnt/juno_mapping - name: Cache minikraken id: cache-minikraken uses: actions/cache@v3 From ff69a2f19dad95f0dc4c8e97e83818565ebdcac5 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 17:13:27 +0100 Subject: [PATCH 12/15] ci: more storage tests --- .github/workflows/juno_mapping_singularity.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index c3dd571..70fadf9 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -85,6 +85,8 @@ jobs: df -h . echo "Checking space: /mnt" df -h /mnt - du -sh /mnt/juno_mapping du -sh /mnt/kraken-database - du -sh ${{ env.GITHUB_WORKSPACE }} \ No newline at end of file + echo "Checking space: $GITHUB_WORKSPACE" + du -sh $GITHUB_WORKSPACE + echo "Checking space: /home/runner" + du -sh /home/runner/* \ No newline at end of file From a50065b0f0e92c4ff788b0c98def2bfdb92f6b99 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Tue, 6 Feb 2024 17:33:15 +0100 Subject: [PATCH 13/15] ci: update test --- tests/test_juno_mapping.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_juno_mapping.py b/tests/test_juno_mapping.py index 041ccbf..b767351 100644 --- a/tests/test_juno_mapping.py +++ b/tests/test_juno_mapping.py @@ -147,7 +147,7 @@ def test_junomapping_dryrun_changed_user_params(self) -> None: "--reference", "reference.fasta", "--disable-mask", - "-maf", + "-smaf", "0.5", "-md", "20", @@ -159,7 +159,7 @@ def test_junomapping_dryrun_changed_user_params(self) -> None: expected_user_param_values = { "species": "mycobacterium_tuberculosis", "reference": "reference.fasta", - "minimum_allele_frequency": 0.5, + "soft_filter_minimum_allele_frequency": 0.5, "minimum_depth": 20, "disable_mask": "True", "mask_bed": "None", From 7548d5a1071aef10509221053b4e5eacd3e3d490 Mon Sep 17 00:00:00 2001 From: boasvdp Date: Wed, 7 Feb 2024 09:02:45 +0100 Subject: [PATCH 14/15] ci: fix wrapper test --- tests/test_juno_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_juno_mapping.py b/tests/test_juno_mapping.py index b767351..fdaf8a7 100644 --- a/tests/test_juno_mapping.py +++ b/tests/test_juno_mapping.py @@ -122,7 +122,7 @@ def test_junomapping_dryrun_user_params(self) -> None: expected_user_param_values = { "species": "mycobacterium_tuberculosis", "reference": "reference.fasta", - "minimum_allele_frequency": 0.8, + "soft_filter_minimum_allele_frequency": 0.8, "minimum_depth": 10, "disable_mask": "False", "mask_bed": "files/RLC_Farhat.bed", From e563cabdb826a239c5790321a773ef2e68a0162c Mon Sep 17 00:00:00 2001 From: boasvdp Date: Wed, 7 Feb 2024 09:22:27 +0100 Subject: [PATCH 15/15] ci: sing e2e on dispatch instead of PR --- .github/workflows/juno_mapping_singularity.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/juno_mapping_singularity.yaml b/.github/workflows/juno_mapping_singularity.yaml index 70fadf9..854afb6 100644 --- a/.github/workflows/juno_mapping_singularity.yaml +++ b/.github/workflows/juno_mapping_singularity.yaml @@ -2,7 +2,7 @@ name: Singularity e2e test -on: [pull_request] +on: workflow_dispatch env: KRAKEN_DEFAULT_DB: /mnt/kraken-database