Use gzip instead of pigz for kraken2 output compression

CHANGELOG.md

@@ -28,6 +28,8 @@ situations.
   container specifications for most rules. This also enables easier use of
   local copies of containers (e.g. in HPC environments without external network
   access).
+- Changed compression of kraken2 host removal artifacts to use gzip instead of
+  pigz due to the latter not being present in the kraken2 biocontainer.
 
 ### Deprecated
 

workflow/rules/preproc/host_removal.smk

@@ -79,8 +79,7 @@ if config["host_removal"]["kraken2"]:
                 {params.extra} \
                 {input.read1} {input.read2} \
                 2> {log.stderr}
-            pigz \
-                --processes {threads} \
+            gzip \
                 --verbose \
                 --force \
                 {params.fq_to_compress} \