From b9bcf9ba33f0ec807a21716b80913ed2f3d97284 Mon Sep 17 00:00:00 2001
From: iborra <paula.iborradetoledo@unibas.ch>
Date: Sun, 3 Jan 2021 22:19:32 +0100
Subject: [PATCH] updated
---
RUN_JOB/config.yaml | 12 ++++++------
RUN_JOB/run_workflow_local.sh | 3 +--
RUN_JOB1/run_workflow_slurm.sh | 2 +-
test/test_dag.sh | 2 --
test/test_rule_graph.sh | 2 --
5 files changed, 8 insertions(+), 13 deletions(-)
diff --git a/RUN_JOB/config.yaml b/RUN_JOB/config.yaml
index 81ff89a..44ea459 100644
--- a/RUN_JOB/config.yaml
+++ b/RUN_JOB/config.yaml
@@ -3,18 +3,18 @@
### Inputs
##############################################################################
# List of "organism/prefix"
- organism: ["Homo_sapiens/GRCh38"]
+ organism: ["ORGANISM/PREFIX"]
#################### PARAMETERS SPECIFIC TO ORGANISM #########################
- Homo_sapiens/GRCh38: {
- genome_url: "ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz",
- gtf_url: "ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz",
- mirna_url: "ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3",
+ ORGANISM/PREFIX: {
+ genome_url: " ##### ",
+ gtf_url: " ##### ",
+ mirna_url: " ##### ",
# Dictionary chromosome/contig name mappings between UCSC <-> Ensembl
# Other organisms available at: https://github.com/dpryan79/ChromosomeMappings
- map_chr_url: "https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/GRCh38_UCSC2ensembl.txt",
+ map_chr_url: " ##### ",
# Chromosome names mapping parameters:
column: 1, #column number from input file where to change chromosome name
delimiter: "TAB" #delimiter of the input file
diff --git a/RUN_JOB/run_workflow_local.sh b/RUN_JOB/run_workflow_local.sh
index 5762dad..9194f41 100755
--- a/RUN_JOB/run_workflow_local.sh
+++ b/RUN_JOB/run_workflow_local.sh
@@ -35,12 +35,11 @@ snakemake \
--printshellcmds \
--snakefile="../workflow/Snakefile" \
--configfile="config.yaml" \
- --cluster-config="cluster.json" \
+ --jobscript="../scripts/jobscript.sh" \
--use-singularity \
--singularity-args "--bind ${PWD},${PWD}/../" \
--cores=4 \
--rerun-incomplete \
- --configfile config.yaml \
--verbose
# Snakemake report
diff --git a/RUN_JOB1/run_workflow_slurm.sh b/RUN_JOB1/run_workflow_slurm.sh
index e4f46f5..9a41218 100755
--- a/RUN_JOB1/run_workflow_slurm.sh
+++ b/RUN_JOB1/run_workflow_slurm.sh
@@ -1,6 +1,6 @@
#!/bin/bash
-# Tear down test environment
+# Tear down environment
cleanup () {
rc=$?
rm -rf .snakemake/
diff --git a/test/test_dag.sh b/test/test_dag.sh
index b8ed111..cd0676f 100755
--- a/test/test_dag.sh
+++ b/test/test_dag.sh
@@ -3,8 +3,6 @@
# Tear down test environment
cleanup () {
rc=$?
- #rm -rf .snakemake
- #rm -rf logs/
cd $user_dir
echo "Exit status: $rc"
}
diff --git a/test/test_rule_graph.sh b/test/test_rule_graph.sh
index 7bcaa3c..3f4365b 100755
--- a/test/test_rule_graph.sh
+++ b/test/test_rule_graph.sh
@@ -3,8 +3,6 @@
# Tear down test environment
cleanup () {
rc=$?
- #rm -rf .snakemake
- #rm -rf logs/
cd $user_dir
echo "Exit status: $rc"
}
--
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