From 769a90a614df6076f40d8e1728fbd01de6ad6e71 Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 14 Nov 2024 08:42:06 +0100 Subject: [PATCH] update workflow --- src/depiction_targeted_preproc/workflow/rules/rules_qc.smk | 3 +++ src/depiction_targeted_preproc/workflow/rules/rules_vis.smk | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk b/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk index 2065d70..75ea05a 100644 --- a/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk +++ b/src/depiction_targeted_preproc/workflow/rules/rules_qc.smk @@ -1,3 +1,6 @@ +# TODO some of these might be more relevant if only using `calibration.csv`, i.e. excluding standards + + rule qc_table_marker_surroundings_baseline: input: imzml=multiext("{sample}/processed", ".imzML", ".ibd"), diff --git a/src/depiction_targeted_preproc/workflow/rules/rules_vis.smk b/src/depiction_targeted_preproc/workflow/rules/rules_vis.smk index 5c24d35..eb590bf 100644 --- a/src/depiction_targeted_preproc/workflow/rules/rules_vis.smk +++ b/src/depiction_targeted_preproc/workflow/rules/rules_vis.smk @@ -2,7 +2,7 @@ rule vis_images: input: imzml=multiext("{sample}/calibrated", ".imzML", ".ibd"), config="{sample}/pipeline_params.yml", - mass_list="{sample}/panels/full.csv", + mass_list="{sample}/panels/full_visualize.csv", output: hdf5="{sample}/images_default.hdf5", # TODO how can i pass n-jobs nicely here