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ktmeaton · Oct 30, 2020 · 573931c · 573931c
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diff --git a/docs-new/main.md b/docs-new/main.md
@@ -54,8 +54,32 @@ TBD
 
 ## Genomic Alignment
 
-Edit ```config/snakemake.yaml``` to increase the number of assembly downloads.
+
+### Modern Assembly
+
+Construct an alignment of ALL modern *Y. pestis* assemblies. Modify ```config/snakemake.yaml``` to have the following lines:
+
 
 ```bash
+max_datasets_assembly : 600
+sqlite_select_command_asm : SELECT
+                               AssemblyFTPGenbank
+                             FROM
+                               BioSample
+                               LEFT JOIN Assembly
+                                 ON AssemblyBioSampleAccession = BioSampleAccession
+                                 WHERE (BioSampleComment LIKE '%Assembly%Modern%')
+```
+
+Construct the pairwise alignment to the reference genome.
 
+```bash
+snakemake --profile profiles/infoserv snippy_pairwise_assembly
 ```
+
+Create a MultiQC report of the genome alignment statistics.
+
+```bash
+snakemake --profile profiles/infoserv multiqc_assembly
+```
+
diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
@@ -32,17 +32,15 @@ rule multiqc:
     """
     input:
         multiqc_config = config_dir + "/multiqc.yaml",
-        qualimap_asm_dir = expand(results_dir + "/qualimap/assembly/{sample}/", sample=identify_assembly_sample()),
-        #qualimap_local_dir = expand(results_dir + "/eager/local/{sample}/qualimap/{sample}/", sample=identify_local_sample()),
-        qualimap_local_dir = expand(results_dir + "/qualimap/local/{sample}/", sample=identify_local_sample()),
-        #qualimap_sra_dir = expand(results_dir + "/eager/sra/{sample}/qualimap/{sample}/", sample=identify_sra_sample()),
-        qualimap_sra_dir = expand(results_dir + "/qualimap/sra/{sample}/", sample=identify_sra_sample()),
-        snippy_multi_txt = results_dir + "/snippy_multi/snippy-core.txt",
-        snippy_asm_dir = expand(results_dir + "/snippy_pairwise/assembly/{sample}/", sample=identify_assembly_sample()),
-        snippy_local_dir = expand(results_dir + "/snippy_pairwise/local/{sample}/", sample=identify_local_sample()),
-        snippy_sra_dir = expand(results_dir + "/snippy_pairwise/sra/{sample}/", sample=identify_sra_sample()),
+        qualimap_dir = lambda wildcards: expand(results_dir + "/qualimap/{{reads_origin}}/{sample}/",
+                       sample=file_acc=globals()["identify_" + wildcards.reads_origin + "_sample"]()),
+        snippy_pairwise_dir = lambda wildcards: expand(results_dir + "/snippy_pairwise/{{reads_origin}}/{sample}/",
+                              sample=file_acc=globals()["identify_" + wildcards.reads_origin + "_sample"]()),
+        snippy_multi_dir = results_dir + "/snippy_multi/",
+    wildcard_constraints:
+        reads_origin="(assembly|sra|local)",
     output:
-        report(results_dir + "/multiqc/multiqc_report.html",
+        multiqc_report = report(results_dir + "/multiqc/multiqc_{reads_origin}.html",
                 caption=os.path.join(report_dir,"multiqc_report.rst"),
                 category="Quality Control",
                 subcategory="MultiQC"),
@@ -68,19 +66,16 @@ rule multiqc:
                 subcategory="Qualimap"),
         dir = directory(results_dir + "/multiqc/"),
     log:
-        os.path.join(logs_dir, "multiqc/multiqc.log")
+        os.path.join(logs_dir, "multiqc/multiqc_{reads_origin}.log")
     resources:
         cpus = 1,
     shell:
         "multiqc \
           -c {input.multiqc_config} \
           --export \
           --outdir {output.dir} \
+          --filename {output.multiqc_report} \
           --force \
-          {input.qualimap_asm_dir} \
-          {input.qualimap_local_dir} \
-          {input.qualimap_sra_dir} \
-          {input.snippy_multi_txt} \
-          {input.snippy_asm_dir} \
-          {input.snippy_local_dir} \
-          {input.snippy_sra_dir} 2> {log}"
+          {input.qualimap_dir} \
+          {input.snippy_pairwise_dir} \
+          {input.snippy_multi_dir} 2> {log}"
diff --git a/workflow/rules/targets.smk b/workflow/rules/targets.smk
@@ -128,8 +128,17 @@ rule qualimap_local:
         expand(results_dir + "/qualimap/local/{sample}/qualimapReport.html",
         sample=identify_local_sample())
 
-# multiqc can be run for testing as
-# rule: iqtree
+rule multiqc_assembly:
+    input:
+        results_dir + "/multiqc/multiqc_assembly.html",
+
+rule multiqc_sra:
+    input:
+        results_dir + "/multiqc/multiqc_sra.html",
+
+rule multiqc_local:
+    input:
+        results_dir + "/multiqc/multiqc_local.html",
 
 #------------------------------------------------------------------------------#
 # Plot