From 8af815fbeeb2d8a57da0b53589967203ed1d8366 Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Fri, 12 Jun 2020 11:59:38 +0200
Subject: [PATCH] fix: added arguments for fragment size mean and sd required
for the salmon quantification approach in single-end mode
---
.gitignore | 1 +
.gitlab-ci.yml | 4 ++--
workflow/rules/single_end.snakefile.smk | 8 +++++++-
3 files changed, 10 insertions(+), 3 deletions(-)
diff --git a/.gitignore b/.gitignore
index 937346f..53dc92e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -328,6 +328,7 @@ pip-selfcheck.json
.DS_Store
runs/.*
!runs/PUT_YOUR_WORKFLOW_RUN_CONFIGS_HERE
+._*
._.DS_Store
.snakemake/
logs/
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dfb1dd4..4913033 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,8 +12,8 @@ test:
# add code quality tests here
# add unit tests here
# add script tests here
- #- bash tests/test_scripts_labkey_to_snakemake_table/test.sh
- #- bash tests/test_scripts_labkey_to_snakemake_api/test.sh
+ # - bash tests/test_scripts_labkey_to_snakemake_table/test.sh
+ # - bash tests/test_scripts_labkey_to_snakemake_api/test.sh
- bash tests/test_alfa/test.sh
# add integration tests here
- bash tests/test_create_dag_image/test.sh
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 0aac065..41e5062 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -237,7 +237,11 @@ rule quantification_salmon:
"{sample}",
"{sample}.salmon.se"),
libType = lambda wildcards:
- samples_table.loc[wildcards.sample, "libtype"]
+ samples_table.loc[wildcards.sample, "libtype"],
+ fraglen = lambda wildcards:
+ samples_table.loc[wildcards.sample, 'mean'],
+ fragsd = lambda wildcards:
+ samples_table.loc[wildcards.sample, 'sd']
log:
stderr = os.path.join(
@@ -262,6 +266,8 @@ rule quantification_salmon:
--seqBias \
--validateMappings \
--threads {threads} \
+ --fldMean {params.fraglen} \
+ --fldSD {params.fragsd} \
--writeUnmappedNames \
--index {input.index} \
--geneMap {input.gtf} \
--
GitLab