feat!: Pin wrapper versions in meta-wrappers; add alignoth_report meta-wrapper

meta/bio/alignoth_report/meta.yaml

@@ -0,0 +1,5 @@
+name: alignoth_report
+description: Export variants via vembrane and create alignment plots with alignoth for a Datavzrd report.
+authors:
+  - Felix Wiegand
+  - Felix Mölder

meta/bio/alignoth_report/meta_wrapper.smk

@@ -0,0 +1,68 @@
+import pandas as pd
+
+checkpoint vembrane_table:
+    input:
+        "<results>/{sample}.bcf",
+    output:
+        "<results>/tables/{sample}.tsv"
+    log:
+        "<logs>/vembrane_table/{sample}.log"
+    params:
+        expression="INDEX, CHROM, POS, ALT, REF",
+        extra=""
+    wrapper:
+        "master/bio/vembrane/table"
+
+
+rule alignoth:
+    input:
+        bam="<results>/mapped/{sample}.bam",
+        reference="resources/genome.fa",
+        vcf="<results>/{sample}.bcf",
+        idx="<results>/{sample}.bcf.csi",
+        overview="<results>/tables/{sample}.tsv"
+    output:
+        directory("<results>/alignoth/{sample}/{index}/")
+    params:
+        extra=lambda wc, input: f"--around {get_variant_position(wc, input)} -f tsv"
+    log:
+        "<logs>/alignoth/{sample}_{index}.log"
+    wrapper:
+        "master/bio/alignoth"
+
+
+rule datavzrd:
+    input:
+        config=workflow.source_path("resources/template.datavzrd.yaml"),
+        overview="<results>/tables/{sample}.tsv",
+        plot_tables=lambda wc: get_alignoth_tables(wc, "results")
+    output:
+        report(
+            directory("<results>/datavzrd-report/{sample}"),
+            htmlindex="index.html",
+        ),
+        # config = "resources/datavzrd/{sample}.rendered_config.yaml"
+    params:
+        max_index=lambda wc: count_variants(wc)
+    log:
+        "<logs>/datavzrd/{sample}.log",
+    wrapper:
+        "master/utils/datavzrd"
+
+
+def get_alignoth_tables(wildcards, results_dir):
+    count = count_variants(wildcards)
+    l = [f"{results_dir}/alignoth/{{sample}}/{i}/" for i in range(count)]
+    return l
+
+
+def count_variants(wildcards):
+    return sum(1 for _ in open(checkpoints.vembrane_table.get(sample=wildcards.sample).output[0], "r")) - 1
+
+
+def get_variant_position(wildcards, input):
+    df = pd.read_csv(input.overview, sep="\t")
+    row = int(wildcards.index)
+    chrom = df.iloc[row]["CHROM"]
+    pos = df.iloc[row]["POS"]
+    return f"{chrom}:{pos}"

meta/bio/alignoth_report/resources/template.datavzrd.yaml

@@ -0,0 +1,58 @@
+__use_yte__: true
+
+default-view: variants
+
+datasets:
+  variants:
+    path: ?input.overview
+    separator: "\t"
+    links:
+        alignment plot:
+          column: INDEX
+          view: "{value}"
+  ?for i in range(params.max_index):
+    ?f"{i}.coverage":
+      path: ?f"{input.plot_tables[i]}/{wildcards.sample}.coverage.tsv"
+      separator: "\t"
+    ?f"{i}.reference":
+      path: ?f"{input.plot_tables[i]}/{wildcards.sample}.reference.tsv"
+      separator: "\t"
+    ?f"{i}.reads":
+      path: ?f"{input.plot_tables[i]}/{wildcards.sample}.reads.tsv"
+      separator: "\t"
+    ?f"{i}.highlight":
+      path: ?f"{input.plot_tables[i]}/{wildcards.sample}.highlight.tsv"
+      separator: "\t"
+views:
+  variants:
+    dataset: variants
+    render-table:
+      columns:
+        INDEX:
+          display-mode: hidden
+        REF:
+          label: reference
+          plot:
+            pills:
+              separator: ""
+              domain: ["A", "T", "G", "C"]
+              range: ["#CADB69", "#7284A8", "#F28CC2", "#F2B671"]
+              merge: true
+        ALT:
+          label: alternative
+          plot:
+            pills:
+              separator: ""
+              domain: ["A", "T", "G", "C"]
+              range: ["#CADB69", "#7284A8", "#F28CC2", "#F2B671"]
+              merge: true
+  ?for i in range(params.max_index):
+    ?i:
+        hidden: true
+        datasets:
+            reads: ?f"{i}.reads"
+            reference: ?f"{i}.reference"
+            coverage: ?f"{i}.coverage"
+            highlight: ?f"{i}.highlight"
+        render-plot:
+            spec-path: ?f"{input.plot_tables[i]}/{wildcards.sample}.vl.json"

meta/bio/alignoth_report/test/Snakefile

@@ -0,0 +1,8 @@
+from snakemake.utils import min_version
+
+min_version("9.13.1")
+
+module alignoth_report:
+    meta_wrapper: "master/meta/bio/alignoth_report"
+
+use rule * from alignoth_report

meta/bio/alignoth_report/test/resources/genome.fa

@@ -0,0 +1,2 @@
+>1
+TGTGCACCCAGGCTAATTAATGTTCATGGGAACTAATTAGAGCTGACATGTACAGCCAGCCTTTTGCTTACTCTGCGGGATCTTGTTCTGTGTGATTTCTCTAGGGGGAGCCTGCTCACTTTGAGTATTTGATGTATCCATTGCACTCAGCACCCATCACCGGTCTAGCTACCTGCATCCGCAAACCCCTTATAGCCACCTGTTCTCTGGATCGATCCATCCGCCTTTGGAATTATGAAACAAAGTAAGGAATGAAAGGCTTGCCTACTTTATTATGCAAGACCCCAGTTGTGAATTTATGTGAATTATTTTAATTACAGTGTTCCAAACTTTAATTATTTAGAAGCTTTCAGTTGGAAAAGATTTTTAAAAAATCAAGTCAGTCAACCTACCTGTTTCTCACTCTTGCGTGGGCTAGAAAACTACTTTGTGGTTTATTTAATGCTTACCACATGCTAGACACTGGGGACATGAAGAGATGAAGACAACACCTCAGTCTCTCACCTTCTTACATAAACTCCTGGGTCCCTCCAGCTCTCCTATCCCCTTGTTTCCCACAGGAACTGCTCTTTGCTTCAGGGAGCTCTCCAGACCCTTTCTTCCTCATCTTTCTCCCAGGACATCACTATCTCAACCACCCCCAACTCCCTCCTGACTTTACCTTCCAGCACAGCTTCCCTGGGAAGCTCCAACCCTAGGTGGACCCCCACCCCCTACTGTTTTCTTTGTTCTTATGTACAACTTCTGGGGCTTCTGGGGAAAAAATACTTGGACAATACTCATGAATTTTGGAATATAAACAGAGCTATGTCTTCAGCATCGCTAGACCACACCTTGACCAGTCTCCCTATCTACCATGCTCCACGCTGGACATTATCCCCTAATAACCAAGATCTAGAAAAGAGAGGAACCAACAATTGCAAACAGTAGTGTGTCTCAAATACGATGATAACAATATATATCAGATACAGTAGATGACTGGAAGGATTTAGTGAGCTAAGCTTACAATTCAGTAATTGATCTTTTTCACAGCACCCTGGAACTATTTAAGGAATACCAAGAAGAGGCATATTCCATCAGCCTTCATCCATCTGGACACTTCATTGTAGTAGGGTTTGCTGACAAACTACGCCTCATGAATCTACTCATTGATGATATACGTTCTTTCAAAGAATACTCTGTTAGAGGATGCGGAGAGGTAAAAAAAAAACTGCTGAAGACAAAAGTCCAGTTTCTTAGAAAGCCACGGCTGAAATATCAGGAACTAACATGATCTGGGGAGGTGGGACCAAAATCTGTCTTGGAGAACTACAGTGGCTTAAAAAAAGGGGGAAGGAGGAAATCCAGTTATTTTCCCAGCAACCTTATTGAGTATATGGTTCCATCCCCATATTCTTATGTCCACCAGACTATTTCATTGAACCTAAAACCTTGTGAGATCCCCGCTATGATAAGTCCTGTCTGTAATTGTGGAATATTAACAAATATTTTAAAAGAAAAGTAATCTCAGAATCAGAGTCACAGCTAAGAAGGTGAGGTTGGAGACGGAGGAGCCAGGGAAAAATAAGCATCAATGGTGAGAGGTAATAAAGAGCGCATCAGCTTTCCCTGAGGTGTCTTGCAGAAACAAGGCAATGATTTCAGGAATTACTTCCCCGGCTCTGAAACATGCTTCTACAGGCAAAATGATTGCTTGTGGTCCCAACGGCTTAATGATTTGTGGGCCTGACAGTGTCAGCATCTGGCCACTATGAGTTACAGGAATAATGAAAGTGTCTGAAAATGTCAGCCACTCCTCAGTCTCATTTGCACCTTCCCCCCACTCCCACCCTCACACGTAGTTTCAGTCTGAACTCGTTGGGAAAAGCACCTCTTGACTGTAACCTCTAATTAGACTGCTCACTTCCTGCTTGCTTGCTCTCTTGCTGTCTTTCCCTATAGTGTTCCTTTAGCAATGGAGGTCACCTGTTTGCTGCAGTCAATGGAAATGTGATTCACGTTTACACCACCACGAGCCTAGAGAACATCTCAAGCCTGAAAGGACACACAGGGAAGGTAAGTGAGTGAACAGTCTCTGGGGAAACAAGGGGCACGGAGCCAAGTATGCCGCCAGCCAGTGGGATACAGGTGAACAAAAGAGAGATGGTTCCTTTCCTCATGGGTTCACTGTCTACTTGGGGAAAGAGACAATAAAACAAATGCACAGACAAATGTAGTTACTAATTGCAGTTCCACTGAAAGAAAAACATGGTGTTGTTGTGAGAGAAATAATGAAGGGGGCGGCATAATTTAGGTGGCTGTATTTGCAAAGGCTTGGTCCTATAAGAGTGAGTAGGAGTTAATCAGACACAACTGGTGGGGATAATCACTGCAGATAGGGATCCAAAGGCCAGAGATGGGAGACTCATAGG

meta/bio/alignoth_report/test/resources/genome.fa.fai

@@ -0,0 +1 @@
+1	2411	3	2411	2412

meta/bio/alignoth_report/used_wrappers.yaml

@@ -0,0 +1,4 @@
+wrappers:
+  - bio/vembrane/table
+  - bio/alignoth
+  - utils/datavzrd

test_wrappers.py

@@ -256,6 +256,18 @@ def test_alignoth(run):
         ["snakemake", "--cores", "1", "--use-conda", "-F", "out/json_plot.vl.json", "out/plot.html", "output-dir/"],
     )
 
+def test_alignoth_report_meta(run):
+    run(
+        "meta/bio/alignoth_report",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "results/datavzrd-report/NA12878/",
+        ],
+    )
+
 
 def test_miller(run):
     run(