feat: added gfatools wrapper (#512)

* Added gfatools * Fixed docs * Update bio/gfatools/environment.yaml Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
snakemake · Aug 16, 2022 · 2c6b897 · 2c6b897
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diff --git a/bio/gfatools/environment.yaml b/bio/gfatools/environment.yaml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - gfatools =0.5
diff --git a/bio/gfatools/meta.yaml b/bio/gfatools/meta.yaml
@@ -0,0 +1,12 @@
+name: gfatools
+description: |
+  Tools for manipulating sequence graphs in the GFA and rGFA formats
+url: https://github.com/lh3/gfatools
+authors:
+  - Filipe G. Vieira
+input:
+  - GFA file
+output:
+  - GFA/stats/FAS/BED/ASM/SQL/TXT (depends on command)
+notes: |
+  * The `command` param allows to specify how to do with the GFA: `view` [default], `stat`, `gfa2fa`, `gfa2bed`, `blacklist`, `bubble`, `asm`, `sql`, or `version`.
diff --git a/bio/gfatools/test/Snakefile b/bio/gfatools/test/Snakefile
@@ -0,0 +1,92 @@
+rule gfatools_stat:
+    input:
+        "{sample}.gfa",
+    output:
+        "{sample}.stat",
+    log:
+        "logs/{sample}.stat.log",
+    params:
+        command="stat",
+    wrapper:
+        "master/bio/gfatools"
+
+
+rule gfatools_gfa2fa:
+    input:
+        "{sample}.gfa",
+    output:
+        "{sample}.fas",
+    log:
+        "logs/{sample}.gfa2fa.log",
+    params:
+        command="gfa2fa",
+	extra="-l 90",
+    wrapper:
+        "master/bio/gfatools"
+
+
+rule gfatools_gfa2bed:
+    input:
+        "{sample}.gfa",
+    output:
+        "{sample}.bed",
+    log:
+        "logs/{sample}.gfa2bed.log",
+    params:
+        command="gfa2bed",
+    wrapper:
+        "master/bio/gfatools"
+
+
+rule gfatools_blacklist:
+    input:
+        "{sample}.gfa",
+    output:
+        "{sample}.blacklist",
+    log:
+        "logs/{sample}.blacklist.log",
+    params:
+        command="blacklist",
+	extra="-l 100",
+    wrapper:
+        "master/bio/gfatools"
+
+
+rule gfatools_bubble:
+    input:
+        "{sample}.gfa",
+    output:
+        "{sample}.bubble",
+    log:
+        "logs/{sample}.bubble.log",
+    params:
+        command="bubble",
+    wrapper:
+        "master/bio/gfatools"
+
+
+rule gfatools_asm:
+    input:
+        "{sample}.gfa",
+    output:
+        "{sample}.asm",
+    log:
+        "logs/{sample}.asm.log",
+    params:
+        command="asm",
+	extra="-u",
+    wrapper:
+        "master/bio/gfatools"
+
+
+rule gfatools_sql:
+    input:
+        "{sample}.gfa",
+    output:
+        "{sample}.sql",
+    log:
+        "logs/{sample}.sql.log",
+    params:
+        command="sql",
+    wrapper:
+        "master/bio/gfatools"