From 1afe738bf1805810d055fc85ad399cd3b5fb9b59 Mon Sep 17 00:00:00 2001 From: "simonescrima@gmail.com" Date: Thu, 6 Aug 2026 12:07:51 +0200 Subject: [PATCH 1/2] Tried to delete bam_filtration rule --- src/mmaseq/workflow/rules/Analysis.smk | 40 +++++++++++++------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/src/mmaseq/workflow/rules/Analysis.smk b/src/mmaseq/workflow/rules/Analysis.smk index 3534378..80955bf 100644 --- a/src/mmaseq/workflow/rules/Analysis.smk +++ b/src/mmaseq/workflow/rules/Analysis.smk @@ -479,26 +479,26 @@ rule samtools_sam_filtration: """ -rule samtools_bam_filtration: - input: - bam = f"{outdir}/{{sample}}/raw/samtools/{{database}}.bam" - params: - options = lambda wc: sample_configs[wc.sample]["samtools"]["view_options"] - output: - results = temp(f"{outdir}/{{sample}}/raw/samtools/samtools_bam_filtration_{{database}}.bam") - conda: - ENVS_DIR / "samtools.yaml" - log: - stdout = f"{logdir}/samtools_bam_filtration_{{database}}_{{sample}}.log" - message: - "[samtools_bam_filtration]: Filtering kmeralignment output for {wildcards.database} on {wildcards.sample}" - shell: - """ - cmd="samtools view {input.bam} {params.options} -F 4 -bo {output.results}" - - echo "Executing command:\n$cmd\n" > {log.stdout} 2>&1 - eval $cmd >> {log.stdout} 2>&1 - """ +# rule samtools_bam_filtration: +# input: +# bam = f"{outdir}/{{sample}}/raw/samtools/{{database}}.bam" +# params: +# options = lambda wc: sample_configs[wc.sample]["samtools"]["view_options"] +# output: +# results = temp(f"{outdir}/{{sample}}/raw/samtools/samtools_bam_filtration_{{database}}.bam") +# conda: +# ENVS_DIR / "samtools.yaml" +# log: +# stdout = f"{logdir}/samtools_bam_filtration_{{database}}_{{sample}}.log" +# message: +# "[samtools_bam_filtration]: Filtering kmeralignment output for {wildcards.database} on {wildcards.sample}" +# shell: +# """ +# cmd="samtools view {input.bam} {params.options} -F 4 -bo {output.results}" + +# echo "Executing command:\n$cmd\n" > {log.stdout} 2>&1 +# eval $cmd >> {log.stdout} 2>&1 +# """ rule samtools_sort: From bf0d752175262e7d9a64b90f8c1e104b7b6de12d Mon Sep 17 00:00:00 2001 From: "simonescrima@gmail.com" Date: Thu, 6 Aug 2026 12:49:55 +0200 Subject: [PATCH 2/2] Deleted the rule --- src/mmaseq/workflow/rules/Analysis.smk | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/src/mmaseq/workflow/rules/Analysis.smk b/src/mmaseq/workflow/rules/Analysis.smk index 80955bf..8871708 100644 --- a/src/mmaseq/workflow/rules/Analysis.smk +++ b/src/mmaseq/workflow/rules/Analysis.smk @@ -479,27 +479,6 @@ rule samtools_sam_filtration: """ -# rule samtools_bam_filtration: -# input: -# bam = f"{outdir}/{{sample}}/raw/samtools/{{database}}.bam" -# params: -# options = lambda wc: sample_configs[wc.sample]["samtools"]["view_options"] -# output: -# results = temp(f"{outdir}/{{sample}}/raw/samtools/samtools_bam_filtration_{{database}}.bam") -# conda: -# ENVS_DIR / "samtools.yaml" -# log: -# stdout = f"{logdir}/samtools_bam_filtration_{{database}}_{{sample}}.log" -# message: -# "[samtools_bam_filtration]: Filtering kmeralignment output for {wildcards.database} on {wildcards.sample}" -# shell: -# """ -# cmd="samtools view {input.bam} {params.options} -F 4 -bo {output.results}" - -# echo "Executing command:\n$cmd\n" > {log.stdout} 2>&1 -# eval $cmd >> {log.stdout} 2>&1 -# """ - rule samtools_sort: input: