changing pipeline name

clemente-lab · Aug 8, 2024 · 82b3919 · 82b3919
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commit 82b3919
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diff --git a/mmeds/snakemake/workflows/core_pipeline_taxonomic.Snakefile b/mmeds/snakemake/workflows/core_pipeline_taxonomic.Snakefile
@@ -0,0 +1,18 @@
+configfile: "config_file.yaml"
+report: "report.rst"
+
+include: "{snakemake_dir}/common.smk"
+include: "{snakemake_dir}/demux_denoise.smk"
+include: "{snakemake_dir}/process_sequencing_data.smk"
+include: "{snakemake_dir}/diversity_analysis.smk"
+include: "{snakemake_dir}/taxonomy.smk"
+include: "{snakemake_dir}/differential_abundance.smk"
+include: "{snakemake_dir}/table_filtering.smk"
+
+rule results:
+    input:
+        expand("diversity/ANOVA/{{metric}}_group_ANOVA.qzv", metric=config['alpha_metrics']),
+        expand("diversity/PERMANOVA/{{var}}/{{metric}}_{{var}}_PERMANOVA.qzv", metric=config['beta_metrics'], var=config['metadata']),
+        "diversity/alpha_rarefaction.qzv",
+        "tables/taxa_barplot.qzv",
+        expand("differential_abundance/{{var}}/ancom-bc_{{table}}_{{var}}_barplot.qzv", table=expand("taxa_table_L{{level}}", level=config['taxa_levels']), var=config['metadata'])
diff --git a/test_files/test_snakemake/core_pipeline_taxonomic/core_pipeline_taxonomic.Snakefile b/test_files/test_snakemake/core_pipeline_taxonomic/core_pipeline_taxonomic.Snakefile
@@ -0,0 +1,20 @@
+configfile: "test_config.yaml"
+report: "report.rst"
+
+include: "snakemake_dir/common.smk"
+include: "snakemake_dir/demux_denoise.smk"
+include: "snakemake_dir/process_sequencing_data.smk"
+include: "snakemake_dir/table_filtering.smk"
+include: "snakemake_dir/diversity_analysis.smk"
+include: "snakemake_dir/taxonomy.smk"
+include: "snakemake_dir/differential_abundance.smk"
+
+rule results:
+    input:
+        expand("diversity/ANOVA/{metric}_group_ANOVA.qzv", metric=config['alpha_metrics']),
+        expand("diversity/PERMANOVA/{var}/{metric}_{var}_PERMANOVA.qzv", metric=config['beta_metrics'], var=config['metadata']),
+        "diversity/alpha_rarefaction.qzv",
+        "tables/taxa_barplot.qzv",
+        expand("tables/taxa_table_L{level}.qza", level=config['taxa_levels']),
+        expand("differential_abundance/{var}/ancom-bc_{table}_{var}_barplot.qzv", table=expand("taxa_table_L{level}", level=config['taxa_levels']), var=config['metadata'])
+
diff --git a/..._snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/for_barcodes.fastq.gz b/..._snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/for_barcodes.fastq.gz
diff --git a/.../test_snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/forward.fastq.gz b/.../test_snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/forward.fastq.gz
diff --git a/..._snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/rev_barcodes.fastq.gz b/..._snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/rev_barcodes.fastq.gz
diff --git a/.../test_snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/reverse.fastq.gz b/.../test_snakemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/import_dir/reverse.fastq.gz
diff --git a/...kemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/qiime_mapping_file_TEST_DUAL_RUN.tsv b/...kemake/core_pipeline_taxonomic/section_TEST_DUAL_RUN/qiime_mapping_file_TEST_DUAL_RUN.tsv
diff --git a/...iles/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/import_dir/barcodes.fastq.gz b/...iles/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/import_dir/barcodes.fastq.gz
diff --git a/...files/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/import_dir/forward.fastq.gz b/...files/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/import_dir/forward.fastq.gz
diff --git a/...files/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/import_dir/reverse.fastq.gz b/...files/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/import_dir/reverse.fastq.gz
diff --git a/...s/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/qiime_mapping_file_TEST_RUN.tsv b/...s/test_snakemake/core_pipeline_taxonomic/section_TEST_RUN/qiime_mapping_file_TEST_RUN.tsv
diff --git a/test_files/test_snakemake/core_pipeline_taxonomic/tables/dummy_classifier.qza b/test_files/test_snakemake/core_pipeline_taxonomic/tables/dummy_classifier.qza
diff --git a/test_files/test_snakemake/core_pipeline_taxonomic/tables/qiime_mapping_file.tsv b/test_files/test_snakemake/core_pipeline_taxonomic/tables/qiime_mapping_file.tsv
diff --git a/test_files/test_snakemake/core_pipeline_taxonomic/test_config.yaml b/test_files/test_snakemake/core_pipeline_taxonomic/test_config.yaml
@@ -0,0 +1,19 @@
+sampling_depth: 1000
+sequencing_runs:
+  - TEST_RUN
+  - TEST_DUAL_RUN
+metadata:
+  - Sex
+  - Group
+alpha_metrics:
+  - faith_pd
+  - observed_features
+beta_metrics:
+  - bray_curtis
+  - unweighted_unifrac
+taxa_levels:
+  - 2
+  - 5
+  - 6
+  - 7
+taxanomic_database: test