feat: added purge_dups wrapper (#528)

* Added purge_dups wrappers

* Fixed typo

* Fixed get_seqs

* Added check for empty bed file

* Fixed missing import

* Fixed linting

* Save warning message to log

* Fixed log typo

* Fixed touch typo

* Update bio/purge_dups/calcuts/environment.yaml

* Update bio/purge_dups/get_seqs/environment.yaml

* Update bio/purge_dups/pbcstat/environment.yaml

* Update bio/purge_dups/ngscstat/environment.yaml

* Update bio/purge_dups/purge_dups/environment.yaml

* Update bio/purge_dups/split_fa/environment.yaml

* Update test.py

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/purge_dups/calcuts/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - purge_dups =1.2

bio/purge_dups/calcuts/meta.yaml

@@ -0,0 +1,11 @@
+name: purge_dups calcuts
+description: Purge haplotigs and overlaps in an assembly based on read depth
+url: https://github.com/dfguan/purge_dups
+authors:
+  - Filipe Vieira
+input:
+  - stats file
+output:
+  - coverage cut-offs
+notes: |
+  * The `extra` param allows for additional program arguments.

bio/purge_dups/calcuts/test/Snakefile

@@ -0,0 +1,12 @@
+rule purge_dups_calcuts:
+    input:
+        "pbcstat.stat",
+    output:
+        "out/calcuts.cutoffs",
+    log:
+        "logs/calcuts.log",
+    params:
+        extra="-l 2 -m 4 -u 8",
+    threads: 1
+    wrapper:
+        "master/bio/purge_dups/calcuts"