From 36c0232888faabd4d01df0b14026ffd75ba3b648 Mon Sep 17 00:00:00 2001
From: BIOPZ-Bak Maciej <maciej.bak@unibas.ch>
Date: Tue, 11 May 2021 08:12:36 +0000
Subject: [PATCH] MultiQC report: custom plugin for zpca. Fixes #146
---
Snakefile | 6 +++---
workflow/scripts/zarp_multiqc_config.py | 20 ++++++++++++++++++++
2 files changed, 23 insertions(+), 3 deletions(-)
diff --git a/Snakefile b/Snakefile
index 588af36..64c346a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1072,7 +1072,7 @@ rule pca_salmon:
threads: 1
singularity:
- "docker://zavolab/zpca:0.8"
+ "docker://zavolab/zpca:0.8.3-1"
shell:
"(zpca-tpm \
@@ -1118,7 +1118,7 @@ rule pca_kallisto:
threads: 1
singularity:
- "docker://zavolab/zpca:0.8"
+ "docker://zavolab/zpca:0.8.3-1"
shell:
"(zpca-tpm \
@@ -1630,7 +1630,7 @@ rule multiqc_report:
current_rule + ".stdout.log")
singularity:
- "docker://zavolab/multiqc-plugins:1.0.0"
+ "docker://zavolab/multiqc-plugins:1.2.1"
shell:
"(multiqc \
diff --git a/workflow/scripts/zarp_multiqc_config.py b/workflow/scripts/zarp_multiqc_config.py
index 40a469e..a78201c 100644
--- a/workflow/scripts/zarp_multiqc_config.py
+++ b/workflow/scripts/zarp_multiqc_config.py
@@ -125,6 +125,26 @@ module_order:
path_filters:
- "*/*/*genome_quantification_kallisto*.stderr.log"
+ - zpca:
+ name: "zpca: salmon | gene expression"
+ path_filters:
+ - "*/zpca/pca_salmon_genes/*"
+
+ - zpca:
+ name: "zpca: salmon | transcript expression"
+ path_filters:
+ - "*/zpca/pca_salmon_transcripts/*"
+
+ - zpca:
+ name: "zpca: kallisto | gene expression"
+ path_filters:
+ - "*/zpca/pca_kallisto_genes/*"
+
+ - zpca:
+ name: "zpca: kallisto | transcript expression"
+ path_filters:
+ - "*/zpca/pca_kallisto_transcripts/*"
+
fn_clean_exts:
- '.fq1'
- '.gz'
--
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