Merge pull request #6 from snakemake-workflows/lint-and-fmt

chore: Address snakemake lints

workflow/envs/bash.yaml

@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - bash =5.1

workflow/rules/annotate.smk

@@ -1,6 +1,3 @@
-CYRCULAR_INFO_FIELDS = ["CircleLength", "CircleSegmentCount", "SplitReads", "Support"]
-
-
 rule extract_vcf_header_lines_for_bcftools_annotate:
     input:
         vcf="results/calling/candidates/{sample}.sorted.bcf",
@@ -39,9 +36,9 @@ rule copy_annotation_from_cyrcular:
     conda:
         "../envs/vcf_annotate.yaml"
     params:
-        header="CHROM,POS,ID,REF,ALT," + ",".join(CYRCULAR_INFO_FIELDS),
-        table_expr="CHROM,POS,ID,REF,ALT," + ",".join(map(lambda s: "INFO['" + s + "']", CYRCULAR_INFO_FIELDS)),
-        columns="CHROM,POS,~ID,REF,ALT," + ",".join(CYRCULAR_INFO_FIELDS),
+        header=copy_annotation_vembrane_header_expr(),
+        table_expr=copy_annotation_table_expr(),
+        columns=copy_annotation_bcftools_annotate_columns(),
     shell:
         """
         vembrane table --header {params.header:q} {params.table_expr:q} {input.candidates_with_annotation} > {output.annotation} 2> {log}

workflow/rules/common.smk

@@ -257,3 +257,21 @@ BND_RE = re.compile(r""".*([]\[])((?P<seqname>.+):(?P<position>[0-9]+))([]\[])?.
 
 def parse_bnd_alt(s: str):
     return BND_RE.search(s)["seqname"], int(BND_RE.search(s)["position"])
+
+
+## rules/annotation.smk specific
+CYRCULAR_INFO_FIELDS = ["CircleLength", "CircleSegmentCount", "SplitReads", "Support"]
+
+
+def copy_annotation_table_expr():
+    return "CHROM,POS,ID,REF,ALT," + ",".join(
+        map(lambda s: f"INFO['{s}']", CYRCULAR_INFO_FIELDS)
+    )
+
+
+def copy_annotation_vembrane_header_expr():
+    return "CHROM,POS,ID,REF,ALT," + ",".join(CYRCULAR_INFO_FIELDS)
+
+
+def copy_annotation_bcftools_annotate_columns():
+    return "CHROM,POS,~ID,REF,ALT," + ",".join(CYRCULAR_INFO_FIELDS)

workflow/rules/datavzrd.smk

@@ -26,11 +26,15 @@ rule copy_qc_plots_for_datavzrd:
         output_dir=lambda wc: directory(
             f"results/datavzrd-report/all.fdr-controlled/circles-{wc.group}/qc_plots"
         ),
+    log:
+        "logs/datavzrd/copy_qc_plots/{group}.log",
+    conda:
+        "../envs/bash.yaml"
     shell:
         """
-        mkdir -p {params.output_dir}
+        mkdir -p {params.output_dir} 2> {log}
         for f in `find {input.plots} -regex '.*/graph_[0-9]+_[0-9]+\.html'`; do ( cp "$f" {params.output_dir} ); done
-        touch {output.marker}
+        touch {output.marker} 2>> {log}
         """
 
 
@@ -44,6 +48,10 @@ rule copy_graph_plots_for_datavzrd:
         output_dir=lambda wc: directory(
             f"results/datavzrd-report/all.fdr-controlled/circles-{wc.group}/graphs"
         ),
+    log:
+        "logs/datavzrd/copy_graph_plots/{group}.log",
+    conda:
+        "../envs/bash.yaml"
     shell:
         """
         mkdir -p {params.output_dir}