From 4baccc984851e42e2fde64f5348e3d292615fe3e Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Fri, 13 Mar 2020 18:13:46 +0100
Subject: [PATCH] fixed snakemake subworkflow typos/bugs
---
workflow/rules/paired_end.snakefile.smk | 1 -
workflow/rules/single_end.snakefile.smk | 6 +-----
2 files changed, 1 insertion(+), 6 deletions(-)
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index c444f46..096f895 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -173,7 +173,6 @@ rule pe_remove_polya_cutadapt:
-n 2 \
-e 0.1 \
-q 6 \
- -m 10 \
-a {params.polya_3_mate1} \
-A {params.polya_3_mate2} \
-o {output.reads1} \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index d2df888..5f9372b 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -15,10 +15,6 @@ rule fastqc:
"{sample}",
"mate1_fastqc"))
- params:
- seqmode = lambda wildcards:
- samples_table.loc[wildcards.sample, "seqmode"]
-
singularity:
"docker://zavolab/fastqc:0.11.9-slim"
@@ -232,7 +228,7 @@ rule map_genome_star:
--outFilterMatchNminOverLread 0.3 \
--outFilterType BySJout \
--outReadsUnmapped None \
- --outSAMattrRGline ID:rcrunch SM:{params.sample_id} \
+ --outSAMattrRGline ID:rnaseq_pipeline SM:{params.sample_id} \
--alignEndsType {params.soft_clip} > {output.bam};) \
2> {log.stderr}"
--
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