latest snakftm firmating

metagenome-atlas · Jul 29, 2024 · 8914ede · 8914ede
1 parent 44415d8
commit 8914ede
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/workflow/rules/assemble.smk b/workflow/rules/assemble.smk
@@ -39,9 +39,9 @@ if SKIP_QC & (len(MULTIFILE_FRACTIONS) < 3):
         params:
             inputs=lambda wc, input: io_params_for_tadpole(input, "in"),
             interleaved=(
-                lambda wc: "t"
-                if (config.get("interleaved_fastqs", False) & SKIP_QC)
-                else "f"
+                lambda wc: (
+                    "t" if (config.get("interleaved_fastqs", False) & SKIP_QC) else "f"
+                )
             ),
             outputs=lambda wc, output: io_params_for_tadpole(output, "out"),
             verifypaired="t" if PAIRED_END else "f",
@@ -456,7 +456,7 @@ else:
     rule rename_spades_output:
         input:
             "{{sample}}/assembly/{sequences}.fasta".format(
-            sequences="scaffolds" if config["spades_use_scaffolds"] else "contigs"
+                sequences="scaffolds" if config["spades_use_scaffolds"] else "contigs"
             ),
         output:
             temp("{sample}/assembly/{sample}_raw_contigs.fasta"),

diff --git a/workflow/rules/binning.smk b/workflow/rules/binning.smk
@@ -141,9 +141,9 @@ rule get_metabat_depth_file:
     resources:
         mem_mb=config["mem"] * 1000,
     params:
-        minid=lambda wc, input: config["cobinning_readmapping_id"] * 100
-        if len(input.bams) > 1
-        else 97,
+        minid=lambda wc, input: (
+            config["cobinning_readmapping_id"] * 100 if len(input.bams) > 1 else 97
+        ),
     shell:
         "jgi_summarize_bam_contig_depths "
         " --percentIdentity {params.minid} "