From fc4e20c8ddfb4c698a89409c3ec4125717d0cac7 Mon Sep 17 00:00:00 2001 From: silask Date: Mon, 29 Jul 2024 12:21:19 +0200 Subject: [PATCH] latest snakftm firmating --- workflow/rules/assemble.smk | 8 ++++---- workflow/rules/binning.smk | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/workflow/rules/assemble.smk b/workflow/rules/assemble.smk index 2ac36e19..7ccd8a93 100644 --- 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 index f3c4aa45..c6d44997 100644 --- 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} "