From 42a636ce218d83255301cef066a7963f4e51be0e Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@udo.edu>
Date: Wed, 14 Sep 2022 12:32:33 +0000
Subject: [PATCH 1/3] move annotation header extraction params to common.smk

---
 workflow/rules/annotate.smk |  9 +++------
 workflow/rules/common.smk   | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/workflow/rules/annotate.smk b/workflow/rules/annotate.smk
index 057d7fb1..c2c461be 100644
--- a/workflow/rules/annotate.smk
+++ b/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}
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 1a27803e..de0d6f17 100644
--- a/workflow/rules/common.smk
+++ b/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)

From 98dff14f999b7f13f3fa926dd708c0f5f4f20b24 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@udo.edu>
Date: Wed, 14 Sep 2022 12:32:57 +0000
Subject: [PATCH 2/3] add missing conda env and log directives

---
 workflow/rules/datavzrd.smk | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk
index 06deaea9..3e3c9975 100644
--- a/workflow/rules/datavzrd.smk
+++ b/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}

From 5be61ca7c6bfd9d9c6681d7c4fc6d0c9c97c035c Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@udo.edu>
Date: Wed, 14 Sep 2022 12:33:38 +0000
Subject: [PATCH 3/3] add bash conda env

---
 workflow/envs/bash.yaml | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 workflow/envs/bash.yaml

diff --git a/workflow/envs/bash.yaml b/workflow/envs/bash.yaml
new file mode 100644
index 00000000..e32d4a8b
--- /dev/null
+++ b/workflow/envs/bash.yaml
@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+  - bash =5.1