screen dryrun worked

metagenome-atlas · Jul 26, 2023 · c157aa6 · c157aa6
1 parent a7e5e00
commit c157aa6
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -41,8 +41,8 @@ wildcard_constraints:
 
 include: "rules/sample_table.smk"
 include: "rules/download.smk"  # contains hard coded variables
-include: "rules/screen.smk"
 include: "rules/qc.smk"
+include: "rules/screen.smk" # expects function get_input_fastq defined in qc
 include: "rules/assemble.smk"
 include: "rules/binning.smk"
 include: "rules/derep.smk"

diff --git a/workflow/rules/screen.smk b/workflow/rules/screen.smk
@@ -18,7 +18,7 @@ rule generate_sketch:
         " samplerate=0.5"
         " minkeycount=2 "
         " out={output} "
-        " blacklist=nt ssu=f name0={sample} depth=t overwrite=t "
+        " blacklist=nt ssu=f name0={wildcards.sample} depth=t overwrite=t "
         " -Xmx{resources.java_mem}g "
         " &> {log}"