From 9ba216b05916710e38f299eb3f091a6388a69ff6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 22 Mar 2024 14:46:00 -0700 Subject: [PATCH] Bump external/pipeline-Nextflow-config from `3ec7186` to `f3448ac` (#145) * Bump external/pipeline-Nextflow-config from `3ec7186` to `f3448ac` Bumps [external/pipeline-Nextflow-config](https://github.com/uclahs-cds/pipeline-Nextflow-config) from `3ec7186` to `f3448ac`. - [Release notes](https://github.com/uclahs-cds/pipeline-Nextflow-config/releases) - [Commits](https://github.com/uclahs-cds/pipeline-Nextflow-config/compare/3ec718630ff1862377815e6c986a8b56cea1115b...f3448ac26989391df434a3d9c59a9227b136431d) --- updated-dependencies: - dependency-name: external/pipeline-Nextflow-config dependency-type: direct:production ... Signed-off-by: dependabot[bot] * Update expected test changes --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Nicholas Wiltsie --- external/pipeline-Nextflow-config | 2 +- test/configtest-F16.json | 185 +----------------------------- 2 files changed, 2 insertions(+), 185 deletions(-) diff --git a/external/pipeline-Nextflow-config b/external/pipeline-Nextflow-config index 3ec7186..f3448ac 160000 --- a/external/pipeline-Nextflow-config +++ b/external/pipeline-Nextflow-config @@ -1 +1 @@ -Subproject commit 3ec718630ff1862377815e6c986a8b56cea1115b +Subproject commit f3448ac26989391df434a3d9c59a9227b136431d diff --git a/test/configtest-F16.json b/test/configtest-F16.json index c46f24a..6dc5065 100644 --- a/test/configtest-F16.json +++ b/test/configtest-F16.json @@ -146,98 +146,6 @@ "verbose": false, "work_dir": "/scratch/523557" }, - "params_schema": { - "algorithm": { - "choices": [ - "delly", - "manta" - ], - "default": [ - "delly", - "manta" - ], - "help": "List of available somatic SV callers", - "required": true, - "type": "List" - }, - "dataset_id": { - "help": "Dataset identifier", - "required": true, - "type": "String" - }, - "exclusion_file": { - "help": "Absoulte path to an exclusion file", - "mode": "r", - "required": true, - "type": "Path" - }, - "filter_condition": { - "default": "FILTER=\\='PASS'", - "help": "", - "required": true, - "type": "String" - }, - "input": { - "elements": { - "BAM": { - "elements": { - "normal": { - "help": "Input normal BAMs", - "required": false, - "type": "BAMEntryList" - }, - "tumor": { - "help": "Input tumor BAMs", - "required": false, - "type": "BAMEntryList" - } - }, - "help": "Input BAMs for somatic structural variant calling", - "required": true, - "type": "InputBAMNamespace" - } - }, - "help": "Input samples", - "required": true, - "type": "InputNamespace" - }, - "mad_cutoff": { - "default": "15", - "help": "", - "required": true, - "type": "Integer" - }, - "map_qual": { - "default": "20", - "help": "", - "required": true, - "type": "Integer" - }, - "min_clique_size": { - "default": "5", - "help": "", - "required": true, - "type": "Integer" - }, - "output_dir": { - "help": "Absolute path to output directory", - "mode": "w", - "required": true, - "type": "Path" - }, - "reference_fasta": { - "help": "Absolute path to a reference FASTA file", - "mode": "r", - "required": true, - "type": "Path" - }, - "sample_id": { - "help": "Sample ID", - "required": true, - "type": "String" - } - }, - "proc_names": "[Ljava.lang.String;@dec0ded", "process": { "cache": false, "commonRetryCodes": [ @@ -374,97 +282,6 @@ "file": "/tmp/outputs/call-sSV-6.1.0/610093/log-call-sSV-6.1.0-19970704T165655Z/nextflow-log/trace.txt" }, "tz": "sun.util.calendar.ZoneInfo[id=\"UTC\",offset=0,dstSavings=0,useDaylight=false,transitions=0,lastRule=null]", - "workDir": "/scratch/523557", - "yaml": { - "algorithm": { - "choices": [ - "delly", - "manta" - ], - "default": [ - "delly", - "manta" - ], - "help": "List of available somatic SV callers", - "required": true, - "type": "List" - }, - "dataset_id": { - "help": "Dataset identifier", - "required": true, - "type": "String" - }, - "exclusion_file": { - "help": "Absoulte path to an exclusion file", - "mode": "r", - "required": true, - "type": "Path" - }, - "filter_condition": { - "default": "FILTER=\\='PASS'", - "help": "", - "required": true, - "type": "String" - }, - "input": { - "elements": { - "BAM": { - "elements": { - "normal": { - "help": "Input normal BAMs", - "required": false, - "type": "BAMEntryList" - }, - "tumor": { - "help": "Input tumor BAMs", - "required": false, - "type": "BAMEntryList" - } - }, - "help": "Input BAMs for somatic structural variant calling", - "required": true, - "type": "InputBAMNamespace" - } - }, - "help": "Input samples", - "required": true, - "type": "InputNamespace" - }, - "mad_cutoff": { - "default": "15", - "help": "", - "required": true, - "type": "Integer" - }, - "map_qual": { - "default": "20", - "help": "", - "required": true, - "type": "Integer" - }, - "min_clique_size": { - "default": "5", - "help": "", - "required": true, - "type": "Integer" - }, - "output_dir": { - "help": "Absolute path to output directory", - "mode": "w", - "required": true, - "type": "Path" - }, - "reference_fasta": { - "help": "Absolute path to a reference FASTA file", - "mode": "r", - "required": true, - "type": "Path" - }, - "sample_id": { - "help": "Sample ID", - "required": true, - "type": "String" - } - } + "workDir": "/scratch/523557" } }